From 8a285bcd99f2d18c7de419c00c13ecd2d9cbd04f Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 28 Apr 2025 13:54:40 -0700 Subject: [PATCH 01/45] Use efetch directory with -id instead of esearch --- rnaseq_pipeline/sources/sra.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index e0e4e63..295ea17 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -99,8 +99,7 @@ class EmptyRunInfoError(Exception): def retrieve_runinfo(sra_accession): """Retrieve a SRA runinfo using search and efetch utilities""" - esearch_proc = Popen(['esearch', '-db', 'sra', '-query', sra_accession], stdout=PIPE) - runinfo_data = check_output(['efetch', '-format', 'runinfo'], universal_newlines=True, stdin=esearch_proc.stdout) + runinfo_data = check_output(['efetch', '-db', 'sra', '-id', sra_accession, '-format', 'runinfo'], universal_newlines=True) if not runinfo_data.strip() or (len(runinfo_data.splitlines()) == 1 and runinfo_data[:3] == 'Run'): raise EmptyRunInfoError(f"Runinfo for {sra_accession} is empty.") return runinfo_data From 4a35d2ba65f5613797806591eb6259a67798194c Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 28 Apr 2025 15:35:11 -0700 Subject: [PATCH 02/45] Use conda-incubator/setup-miniconda --- .github/workflows/build.yml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7e20bc4..70c8928 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,20 +7,16 @@ jobs: runs-on: ubuntu-latest strategy: max-parallel: 5 + defaults: + run: + shell: bash -el {0} steps: - uses: actions/checkout@v4 - - name: Set up Python 3.10 - uses: actions/setup-python@v5 + - uses: conda-incubator/setup-miniconda@v3 with: - python-version: '3.9' - - name: Add conda to system path - run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH - - name: Setup Conda environment - run: | - conda env update --file environment.yml --name base + activate-environment: rnaseq-pipeline + environment-file: environment.yml - name: Install package run: | pip install .[gsheet,webviewer] From 6b21de9fccc7f29d39f3c6db6867ea69af7a7735 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 16 Sep 2025 14:38:01 -0700 Subject: [PATCH 03/45] Fix missing GemmaTaskMixin import --- tests/test_tasks.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/test_tasks.py b/tests/test_tasks.py index 8b898f1..7a04417 100644 --- a/tests/test_tasks.py +++ b/tests/test_tasks.py @@ -1,5 +1,6 @@ import pytest +from gemma import GemmaTaskMixin from rnaseq_pipeline.sources.geo import match_geo_platform from rnaseq_pipeline.tasks import * From 8ad0e47ab845907125a1e595afb56226c20c21f8 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 16 Sep 2025 16:14:18 -0700 Subject: [PATCH 04/45] Skip checking GemmaDatasetHasBatch since it requires credentials --- tests/test_targets.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/test_targets.py b/tests/test_targets.py index 44f1c2e..4015ab7 100644 --- a/tests/test_targets.py +++ b/tests/test_targets.py @@ -2,12 +2,17 @@ from datetime import timedelta from time import sleep +import pytest + from rnaseq_pipeline.targets import GemmaDatasetPlatform, GemmaDatasetHasBatch, ExpirableLocalTarget def test_gemma_targets(): - assert GemmaDatasetHasBatch('GSE110256').exists() assert GemmaDatasetPlatform('GSE110256', 'Generic_mouse_ncbiIds').exists() +@pytest.mark.skip('This test requires credentials.') +def test_gemma_dataset_has_batch(): + assert GemmaDatasetHasBatch('GSE110256').exists() + def test_expirable_local_target(): with tempfile.TemporaryDirectory() as tmp_dir: t = ExpirableLocalTarget(tmp_dir + '/test', ttl=timedelta(seconds=1)) From 960c2a35193216588aa17c9e6f37167569c3a917 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 24 Jun 2025 10:33:04 -0700 Subject: [PATCH 05/45] Add support for single-cell RNA-Seq datasets Parse SRA metadata from its XML format so that we can infer the role that each file plays in fastq-dump output. Add typing and fix many bugs. Retrieve the SRA public dir from a configuration Improve layout detection from SRA metadata Detect bcl2fastq standard filenames and also commonly used names. Add a fallback that checks for the presence of I1/I2/R1/R2, but warns since this is very unreliable. Track issues encountered in runs using an enumerated flag. Make resolution of test resources relative Allow some of the parameters for filtering cells to be overwritten if needed. Use CellRangerCount task from bioluigi Fix unpacking of singleton for single-run experiments Remove cell_ranger_bin from config, it's declared in bioluigi --- README.md | 16 +- example.luigi.cfg | 14 +- find-samples-with-multiple-lanes.py | 81 + pyproject.toml | 6 + pytest.ini | 3 + rnaseq_pipeline/config.py | 27 +- rnaseq_pipeline/gemma.py | 26 +- rnaseq_pipeline/gsheet.py | 5 +- rnaseq_pipeline/platforms.py | 14 +- rnaseq_pipeline/rnaseq_utils.py | 218 + rnaseq_pipeline/sources/arrayexpress.py | 61 +- rnaseq_pipeline/sources/gemma.py | 11 +- rnaseq_pipeline/sources/geo.py | 13 +- rnaseq_pipeline/sources/local.py | 7 +- rnaseq_pipeline/sources/sra.py | 344 +- rnaseq_pipeline/targets.py | 18 + rnaseq_pipeline/tasks.py | 181 +- rnaseq_pipeline/utils.py | 2 +- rnaseq_pipeline/webviewer/__init__.py | 1 - tests/data/GSE104493.xml | 133041 +++++++++++++++++++++ tests/data/GSE125536.xml | 390 + tests/data/GSE128117.xml | 4468 + tests/data/GSE141784.xml | 1937 + tests/data/GSE157985.xml | 1604 + tests/data/GSE163314.xml | 11508 ++ tests/data/GSE173242.xml | 1930 + tests/data/GSE174332.xml | 18154 +++ tests/data/GSE174667.xml | 3706 + tests/data/GSE178257.xml | 2029 + tests/data/GSE179135.xml | 3761 + tests/data/GSE180672.xml | 3856 + tests/data/GSE181021.xml | 1884 + tests/data/GSE181989.xml | 1888 + tests/data/GSE184506.xml | 8980 ++ tests/data/GSE196929.xml | 1449 + tests/data/GSE198891.xml | 2296 + tests/data/GSE202704.xml | 10966 ++ tests/data/GSE205049.xml | 3712 + tests/data/GSE212351.xml | 2430 + tests/data/GSE212505.xml | 1684 + tests/data/GSE212527.xml | 1986 + tests/data/GSE212576.xml | 3297 + tests/data/GSE213364.xml | 1512 + tests/data/GSE214244.xml | 2940 + tests/data/GSE216766.xml | 1548 + tests/data/GSE217511.xml | 8032 ++ tests/data/GSE218316.xml | 1134 + tests/data/GSE218572.xml | 23990 ++++ tests/data/GSE219280.xml | 14522 +++ tests/data/GSE222510.xml | 12716 ++ tests/data/GSE222647.xml | 15034 +++ tests/data/GSE226072.xml | 10372 ++ tests/data/GSE226822.xml | 3473 + tests/data/GSE227515.xml | 3743 + tests/data/GSE230451.xml | 1572 + tests/data/GSE232309.xml | 1764 + tests/data/GSE233276.xml | 2236 + tests/data/GSE234278.xml | 3452 + tests/data/GSE234419.xml | 1069 + tests/data/GSE234421.xml | 1708 + tests/data/GSE235193.xml | 1276 + tests/data/GSE235490.xml | 1700 + tests/data/GSE237816.xml | 5032 + tests/data/GSE240687.xml | 1620 + tests/data/GSE241349.xml | 1264 + tests/data/GSE242271.xml | 3529 + tests/data/GSE245339.xml | 1276 + tests/data/GSE247070.xml | 4108 + tests/data/GSE247695.xml | 1692 + tests/data/GSE247963.xml | 832 + tests/data/GSE249268.xml | 9275 ++ tests/data/GSE253640.xml | 2272 + tests/data/GSE254044.xml | 1700 + tests/data/GSE254104.xml | 11703 ++ tests/data/GSE255460.xml | 3812 + tests/data/GSE261494.xml | 4744 + tests/data/GSE261596.xml | 2608 + tests/data/GSE263191.xml | 3220 + tests/data/GSE263392.xml | 5536 + tests/data/GSE264408.xml | 2164 + tests/data/GSE266033.xml | 4026 + tests/data/GSE267764.xml | 1200 + tests/data/GSE267933.xml | 1312 + tests/data/GSE268343.xml | 1264 + tests/data/GSE268642.xml | 1912 + tests/data/GSE269499.xml | 6332 + tests/data/GSE272062.xml | 1216 + tests/data/GSE272344.xml | 1876 + tests/data/GSE274763.xml | 3136 + tests/data/GSE274829.xml | 1871 + tests/data/GSE275205.xml | 1700 + tests/data/GSE279548.xml | 824 + tests/data/GSE280296.xml | 7650 ++ tests/data/GSE283187.xml | 3044 + tests/data/GSE283268.xml | 3100 + tests/data/GSE284797.xml | 3883 + tests/data/GSE287769.xml | 4634 + tests/data/GSE295459.xml | 2316 + tests/data/GSE296027.xml | 3642 + tests/data/GSE297666.xml | 1114 + tests/data/GSE297721.xml | 12760 ++ tests/data/GSE302153.xml | 6436 + tests/data/SRX26261721.runinfo | 3 + tests/data/SRX26261721.xml | 308 + tests/test_arrayexpress.py | 6 + tests/test_miniml_utils.py | 12 +- tests/test_rnaseq_utils.py | 9 + tests/test_sra.py | 276 +- tests/test_tasks.py | 2 +- tests/test_webviewer.py | 1 + 110 files changed, 483876 insertions(+), 173 deletions(-) create mode 100644 find-samples-with-multiple-lanes.py create mode 100644 pyproject.toml create mode 100644 pytest.ini create mode 100644 rnaseq_pipeline/rnaseq_utils.py create mode 100644 tests/data/GSE104493.xml create mode 100644 tests/data/GSE125536.xml create mode 100644 tests/data/GSE128117.xml create mode 100644 tests/data/GSE141784.xml create mode 100644 tests/data/GSE157985.xml create mode 100644 tests/data/GSE163314.xml create mode 100644 tests/data/GSE173242.xml create mode 100644 tests/data/GSE174332.xml create mode 100644 tests/data/GSE174667.xml create mode 100644 tests/data/GSE178257.xml create mode 100644 tests/data/GSE179135.xml create mode 100644 tests/data/GSE180672.xml create mode 100644 tests/data/GSE181021.xml create mode 100644 tests/data/GSE181989.xml create mode 100644 tests/data/GSE184506.xml create mode 100644 tests/data/GSE196929.xml create mode 100644 tests/data/GSE198891.xml create mode 100644 tests/data/GSE202704.xml create mode 100644 tests/data/GSE205049.xml create mode 100644 tests/data/GSE212351.xml create mode 100644 tests/data/GSE212505.xml create mode 100644 tests/data/GSE212527.xml create mode 100644 tests/data/GSE212576.xml create mode 100644 tests/data/GSE213364.xml create mode 100644 tests/data/GSE214244.xml create mode 100644 tests/data/GSE216766.xml create mode 100644 tests/data/GSE217511.xml create mode 100644 tests/data/GSE218316.xml create mode 100644 tests/data/GSE218572.xml create mode 100644 tests/data/GSE219280.xml create mode 100644 tests/data/GSE222510.xml create mode 100644 tests/data/GSE222647.xml create mode 100644 tests/data/GSE226072.xml create mode 100644 tests/data/GSE226822.xml create mode 100644 tests/data/GSE227515.xml create mode 100644 tests/data/GSE230451.xml create mode 100644 tests/data/GSE232309.xml create mode 100644 tests/data/GSE233276.xml create mode 100644 tests/data/GSE234278.xml create mode 100644 tests/data/GSE234419.xml create mode 100644 tests/data/GSE234421.xml create mode 100644 tests/data/GSE235193.xml create mode 100644 tests/data/GSE235490.xml create mode 100644 tests/data/GSE237816.xml create mode 100644 tests/data/GSE240687.xml create mode 100644 tests/data/GSE241349.xml create mode 100644 tests/data/GSE242271.xml create mode 100644 tests/data/GSE245339.xml create mode 100644 tests/data/GSE247070.xml create mode 100644 tests/data/GSE247695.xml create mode 100644 tests/data/GSE247963.xml create mode 100644 tests/data/GSE249268.xml create mode 100644 tests/data/GSE253640.xml create mode 100644 tests/data/GSE254044.xml create mode 100644 tests/data/GSE254104.xml create mode 100644 tests/data/GSE255460.xml create mode 100644 tests/data/GSE261494.xml create mode 100644 tests/data/GSE261596.xml create mode 100644 tests/data/GSE263191.xml create mode 100644 tests/data/GSE263392.xml create mode 100644 tests/data/GSE264408.xml create mode 100644 tests/data/GSE266033.xml create mode 100644 tests/data/GSE267764.xml create mode 100644 tests/data/GSE267933.xml create mode 100644 tests/data/GSE268343.xml create mode 100644 tests/data/GSE268642.xml create mode 100644 tests/data/GSE269499.xml create mode 100644 tests/data/GSE272062.xml create mode 100644 tests/data/GSE272344.xml create mode 100644 tests/data/GSE274763.xml create mode 100644 tests/data/GSE274829.xml create mode 100644 tests/data/GSE275205.xml create mode 100644 tests/data/GSE279548.xml create mode 100644 tests/data/GSE280296.xml create mode 100644 tests/data/GSE283187.xml create mode 100644 tests/data/GSE283268.xml create mode 100644 tests/data/GSE284797.xml create mode 100644 tests/data/GSE287769.xml create mode 100644 tests/data/GSE295459.xml create mode 100644 tests/data/GSE296027.xml create mode 100644 tests/data/GSE297666.xml create mode 100644 tests/data/GSE297721.xml create mode 100644 tests/data/GSE302153.xml create mode 100644 tests/data/SRX26261721.runinfo create mode 100644 tests/data/SRX26261721.xml create mode 100644 tests/test_arrayexpress.py create mode 100644 tests/test_rnaseq_utils.py diff --git a/README.md b/README.md index 8f541f9..2a1c031 100755 --- a/README.md +++ b/README.md @@ -102,13 +102,15 @@ The output is organized as follow: ``` pipeline-output/ - genomes// # Genomic references - references// # RSEM/STAR indexes - data/ # FASTQs (note that GEO source uses SRA) - data-qc/// # FastQC reports - aligned/// # alignments and quantification results - quantified/ # quantification matrices for isoforms and genes - report/// # MultiQC reports for reads and alignments + genomes// # Genomic references + references// # RSEM/STAR indexes + data// # FASTQs (organization is source-specific; note that GEO source uses SRA) + data-qc/// # FastQC reports + data-single-cell/// # Single-cell data (hard links to files from data/) + aligned/// # alignments and quantification results + quantified/ # quantification matrices for isoforms and genes + quantified-single-cell/ # quantified single-cell data (Cell Ranger outputs) + report/// # MultiQC reports for reads and alignments ``` You can adjust the pipeline output directory by setting `OUTPUT_DIR` under diff --git a/example.luigi.cfg b/example.luigi.cfg index 715e094..5cfa6ea 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -27,9 +27,12 @@ submit_data_jobs=1 submit_batch_info_jobs=2 [bioluigi] -scheduler=slurm +scheduler=local scheduler_partition= scheduler_extra_args=[] +# Default tools, override as needed +#cutadapt_bin=cutadapt +#cell_ranger_bin=cellranger # # This section contains the necessary variables for the pipeline execution @@ -40,6 +43,7 @@ scheduler_extra_args=[] OUTPUT_DIR=pipeline-output GENOMES=genomes REFERENCES=references +SINGLE_CELL_REFERENCES=references-single-cell METADATA=metadata DATA=data DATAQCDIR=data-qc @@ -53,6 +57,11 @@ RSEM_DIR=contrib/RSEM SLACK_WEBHOOK_URL= +[rnaseq_pipeline.sources.sra] +# location where tools like prefetch and fastq-dump will store downloaded SRA files +# you can get this value with vdb-config -p +ncbi_public_dir=/cosmos/scratch/ncbi/public + [rnaseq_pipeline.gemma] cli_bin=gemma-cli # values for $JAVA_HOME and $JAVA_OPTS environment variables @@ -63,3 +72,6 @@ appdata_dir=/space/gemmaData human_reference_id=hg38_ncbi mouse_reference_id=mm10_ncbi rat_reference_id=rn7_ncbi +human_single_cell_reference_id=refdata-gex-GRCh38-2024-A +mouse_single_cell_reference_id=refdata-gex-GRCm39-2024-A +rat_single_cell_reference_id=refdata-gex-mRatBN7-2-2024-A diff --git a/find-samples-with-multiple-lanes.py b/find-samples-with-multiple-lanes.py new file mode 100644 index 0000000..58cf9a4 --- /dev/null +++ b/find-samples-with-multiple-lanes.py @@ -0,0 +1,81 @@ +import tarfile +import tempfile +from io import StringIO +from urllib.parse import urlparse, parse_qs + +import pandas as pd +import requests +from tqdm import tqdm + +from rnaseq_pipeline.miniml_utils import collect_geo_samples_info + +ns = {'miniml': 'http://www.ncbi.nlm.nih.gov/geo/info/MINiML'} + +def retrieve_geo_series_miniml_from_ftp(gse): + res = requests.get(f'https://ftp.ncbi.nlm.nih.gov/geo/series/{gse[:-3]}nnn/{gse}/miniml/{gse}_family.xml.tgz', + stream=True) + res.raise_for_status() + # we need to use a temporary file because Response.raw does not allow seeking + with tempfile.TemporaryFile() as tmp: + for chunk in res.iter_content(chunk_size=1024): + tmp.write(chunk) + tmp.seek(0) + with tarfile.open(fileobj=tmp, mode='r:gz') as fin: + reader = fin.extractfile(f'{gse}_family.xml') + return reader.read().decode('utf-8') + +def retrieve_geo_series_miniml_from_geo_query(gse): + res = requests.get('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi', params=dict(acc=gse, form='xml', targ='gsm')) + res.raise_for_status() + return res.text + +def fetch_sra_metadata(gse): + try: + miniml = retrieve_geo_series_miniml_from_ftp(gse) + except Exception as e: + print( + f'Failed to retrieve MINiML metadata for {gse} from NCBI FTP server will attempt to use GEO directly.', + e) + try: + miniml = retrieve_geo_series_miniml_from_geo_query(gse) + except Exception as e: + print(f'Failed to retrieve MINiML metadata for {gse} from GEO query.', e) + return [] + try: + meta = collect_geo_samples_info(StringIO(miniml)) + except Exception as e: + print('Failed to parse MINiML from input: ' + miniml[:100], e) + return [] + results = [] + for gsm in meta: + platform, srx_url = meta[gsm] + srx = parse_qs(urlparse(srx_url).query)['term'][0] + results.append((gse, gsm, srx)) + return results + +with open('geo-sample-to-sra-experiment.tsv', 'wt') as f: + print('geo_series', 'geo_sample', 'sra_experiment', file=f, sep='\t', flush=True) + df = pd.read_table('gemma-rnaseq-datasets.tsv') + batch = [] + for gse in tqdm(df.geo_accession): + samples = fetch_sra_metadata(gse) + for sample in samples: + print(*sample, file=f, sep='\t', flush=True) + +# def fetch_runinfo(srx_ids): +# # fetch the SRX metadata +# return pd.read_csv(StringIO(retrieve_runinfo(srx_ids))) +# +# def print_results(samples): +# srx_ids = [s[2] for s in samples] +# try: +# results = fetch_runinfo(srx_ids) +# except Exception as e: +# print('Failed to retrieve runinfo for the following SRX IDs:', srx_ids, e) +# return +# for sample in samples: +# runs = results[results['Experiment'] == sample[2]]['Run'] +# r = sample + ('|'.join(runs), len(runs)) +# print(*r, sep='\t', flush=True) +# +# BATCH_SIZE = 100 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..3d86a36 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,6 @@ +[build-system] +requires = ["setuptools"] +build-backend = "setuptools.build_meta" + +[tool.mypy] +plugins = ["luigi.mypy"] diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..18fcdbc --- /dev/null +++ b/pytest.ini @@ -0,0 +1,3 @@ +[pytest] +log_cli=1 +log_cli_level=warning \ No newline at end of file diff --git a/rnaseq_pipeline/config.py b/rnaseq_pipeline/config.py index 3081e4c..6ac3ce6 100644 --- a/rnaseq_pipeline/config.py +++ b/rnaseq_pipeline/config.py @@ -1,21 +1,24 @@ +from typing import Optional + import luigi # see luigi.cfg for details class rnaseq_pipeline(luigi.Config): task_namespace = '' - GENOMES = luigi.Parameter() + GENOMES: str = luigi.Parameter() - OUTPUT_DIR = luigi.Parameter() - REFERENCES = luigi.Parameter() - METADATA = luigi.Parameter() - DATA = luigi.Parameter() - DATAQCDIR = luigi.Parameter() - ALIGNDIR = luigi.Parameter() - ALIGNQCDIR = luigi.Parameter() - QUANTDIR = luigi.Parameter() - BATCHINFODIR = luigi.Parameter() + OUTPUT_DIR: str = luigi.Parameter() + REFERENCES: str = luigi.Parameter() + SINGLE_CELL_REFERENCES: str = luigi.Parameter() + METADATA: str = luigi.Parameter() + DATA: str = luigi.Parameter() + DATAQCDIR: str = luigi.Parameter() + ALIGNDIR: str = luigi.Parameter() + ALIGNQCDIR: str = luigi.Parameter() + QUANTDIR: str = luigi.Parameter() + BATCHINFODIR: str = luigi.Parameter() - RSEM_DIR = luigi.Parameter() + RSEM_DIR: str = luigi.Parameter() - SLACK_WEBHOOK_URL = luigi.OptionalParameter(default=None) + SLACK_WEBHOOK_URL: Optional[str] = luigi.OptionalParameter(default=None) diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py index 13047a7..16346f1 100644 --- a/rnaseq_pipeline/gemma.py +++ b/rnaseq_pipeline/gemma.py @@ -10,14 +10,17 @@ class gemma(luigi.Config): task_namespace = 'rnaseq_pipeline' - baseurl = luigi.Parameter() - appdata_dir = luigi.Parameter() - cli_bin = luigi.Parameter() - cli_JAVA_HOME = luigi.Parameter() - cli_JAVA_OPTS = luigi.Parameter() - human_reference_id = luigi.Parameter() - mouse_reference_id = luigi.Parameter() - rat_reference_id = luigi.Parameter() + baseurl: str = luigi.Parameter() + appdata_dir: str = luigi.Parameter() + cli_bin: str = luigi.Parameter() + cli_JAVA_HOME: str = luigi.Parameter() + cli_JAVA_OPTS: str = luigi.Parameter() + human_reference_id: str = luigi.Parameter() + mouse_reference_id: str = luigi.Parameter() + rat_reference_id: str = luigi.Parameter() + human_single_cell_reference_id: str = luigi.Parameter() + mouse_single_cell_reference_id: str = luigi.Parameter() + rat_single_cell_reference_id: str = luigi.Parameter() cfg = gemma() @@ -98,6 +101,13 @@ def reference_id(self): except KeyError: raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) + def single_cell_reference_id(self): + try: + return {'human': cfg.human_single_cell_reference_id, 'mouse': cfg.mouse_single_cell_reference_id, 'rat': cfg.rat_single_cell_reference_id}[ + self.taxon] + except KeyError: + raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) + @property def platform_short_name(self): return f'Generic_{self.taxon}_ncbiIds' diff --git a/rnaseq_pipeline/gsheet.py b/rnaseq_pipeline/gsheet.py index 43c60d8..16e2e88 100644 --- a/rnaseq_pipeline/gsheet.py +++ b/rnaseq_pipeline/gsheet.py @@ -1,5 +1,4 @@ import logging -import logging import os import os.path import pickle @@ -15,7 +14,7 @@ SCOPES = ['https://www.googleapis.com/auth/spreadsheets.readonly'] CREDENTIALS_FILE = resource_filename('rnaseq_pipeline', 'credentials.json') -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) def _authenticate(): # authentication @@ -41,7 +40,7 @@ def _authenticate(): logger.info(f'Created Google Sheets API token under {token_path}.') return creds -def retrieve_spreadsheet(spreadsheet_id, sheet_name): +def retrieve_spreadsheet(spreadsheet_id: str, sheet_name: str): service = build('sheets', 'v4', credentials=_authenticate(), cache_discovery=None) # Retrieve the documents contents from the Docs service. diff --git a/rnaseq_pipeline/platforms.py b/rnaseq_pipeline/platforms.py index 47d5733..9c50339 100644 --- a/rnaseq_pipeline/platforms.py +++ b/rnaseq_pipeline/platforms.py @@ -1,4 +1,4 @@ -from abc import abstractmethod +from typing import Optional from bioluigi.tasks import cutadapt @@ -6,15 +6,13 @@ class Platform: """ :param name: Platform common name """ - name = None + name: Optional[str] = None - @abstractmethod - def get_trim_single_end_reads_task(r1, dest, **kwargs): - pass + def get_trim_single_end_reads_task(self, r1, dest, **kwargs): + raise NotImplementedError - @abstractmethod - def get_trim_paired_reads_task(r1, r2, r1_dest, r2_dest, **kwargs): - pass + def get_trim_paired_reads_task(self, r1, r2, r1_dest, r2_dest, **kwargs): + raise NotImplementedError class BgiPlatform(Platform): """ diff --git a/rnaseq_pipeline/rnaseq_utils.py b/rnaseq_pipeline/rnaseq_utils.py new file mode 100644 index 0000000..d9575a3 --- /dev/null +++ b/rnaseq_pipeline/rnaseq_utils.py @@ -0,0 +1,218 @@ +""" +Utilities for inferring layouts of RNA-Seq data based on original filenames +""" +import enum +import logging +import re +from typing import Optional + +logger = logging.getLogger(__name__) + +class SequencingFileType(enum.Enum): + """Type of RNA-Seq file""" + I1 = 1 + I2 = 2 + R1 = 3 + R2 = 4 + R3 = 5 + R4 = 6 + +def detect_layout(run_id: str, filenames: Optional[list[str]], + file_sizes: Optional[list[int]] = None, + average_read_lengths: Optional[list[float]] = None, + is_single_end: bool = False, is_paired: bool = False): + """Detects the layout of the sequencing run files based on their names and various additional information. + + :param run_id: Identifier for the run + :param filenames: List of filenames, if known + :param file_sizes: List of file sizes, if known + :param average_read_lengths: List of read lengths (average if variable) for each file, if known + :param is_single_end: Indicate if the sequencing data is single-end (i.e. only R1 is expected to be present). + :param is_paired: Indicate if the sequencing data is paired (i.e. R1 and R2 are expected to be present), this will + be used to resolve ambiguities. + :raises ValueError: If the layout cannot be determined from the filenames. + """ + + if filenames: + if layout := detect_bcl2fastq_name(run_id, filenames): + logger.info('%s: Inferred file types: %s from file names conforming to bcl2fastq output: %s.', run_id, + layout, filenames) + return layout + + if layout := detect_common_fastq_name(run_id, filenames): + logger.info('%s: Inferred file types: %s from file names conforming to a common output.', run_id, + layout, filenames) + return layout + + if layout := detect_fallback_fastq_name(run_id, filenames): + logger.warning('%s: Inferred file types: %s from file names with fallback name patterns: %s. This is highly inaccurate.', + run_id, layout, filenames) + return layout + + number_of_files = len(filenames) + else: + number_of_files = len(average_read_lengths) + + # assume single-end read if only one file is present + if number_of_files == 1: + if is_paired: + raise ValueError( + f'Expected the sequencing data for {run_id} to be paired, but only one file is present.') + return [SequencingFileType.R1] + + # assume paired ends if two files are present + if number_of_files == 2: + if is_single_end: + return order_layout_by_size_information(run_id, [SequencingFileType.I1, SequencingFileType.R1], + file_sizes, average_read_lengths) + else: + return [SequencingFileType.R1, SequencingFileType.R2] + + if number_of_files == 3: + if is_single_end: + return order_layout_by_size_information(run_id, [SequencingFileType.I1, SequencingFileType.I2, + SequencingFileType.R1], file_sizes, + average_read_lengths) + else: + return order_layout_by_size_information(run_id, [SequencingFileType.I1, SequencingFileType.R1, + SequencingFileType.R2], file_sizes, + average_read_lengths) + + if number_of_files == 4: + if is_single_end: + raise ValueError( + f'Expected the sequencing data for {run_id} to be single-ended, but four files are present.') + return order_layout_by_size_information(run_id, [SequencingFileType.I1, SequencingFileType.I2, + SequencingFileType.R1, SequencingFileType.R2], + file_sizes, + average_read_lengths) + + raise ValueError( + f'Unable to detect sequencing layout for {run_id} from: {filenames=} {file_sizes=} {average_read_lengths=} {is_single_end=} {is_paired=}') + +def detect_bcl2fastq_name(run_id, filenames): + # try to detect the file types based on the filenames + # from bcl2fastq manual, this is the expected format of the filenames: + # __L_R_.fastq.gz + bcl2fastq_name_pattern = re.compile(r'(.+)_L0*(\d+)_([RI])(\d)_\d+\.fastq(\.gz)?') + + detected_types = [] + for filename in filenames: + if match := bcl2fastq_name_pattern.match(filename): + sample_name = match.group(1) + lane = match.group(2) + read_type = match.group(3) + read_number = int(match.group(4)) + if read_type == 'I' and read_number == 1: + dt = SequencingFileType.I1 + elif read_type == 'I' and read_number == 2: + dt = SequencingFileType.I2 + elif read_type == 'R' and read_number == 1: + dt = SequencingFileType.R1 + elif read_type == 'R' and read_number == 2: + dt = SequencingFileType.R2 + elif read_type == 'R' and read_number == 3: + dt = SequencingFileType.R3 + elif read_type == 'R' and read_number == 4: + dt = SequencingFileType.R4 + else: + logger.warning('%s: Unrecognized read type: %s%d in %s.', run_id, read_type, read_number, filename) + break + detected_types.append(dt) + + if len(set(detected_types)) < len(detected_types): + logger.warning("%s: Non-unique sequencing file type detected: %s from %s.", run_id, detected_types, filenames) + return None + elif len(detected_types) == len(filenames): + return detected_types + else: + return None + +def detect_common_fastq_name(run_id, filenames): + """Flexible detection of sequencing file types based on common, but valid naming patterns.""" + simple_name_pattern = re.compile(r'(.+[._-])?([RIri])(\d)([._-].+)?\.(fastq|fq)(\.gz)?') + + detected_types = [] + for filename in filenames: + if match := simple_name_pattern.match(filename): + sample_name = match.group(1) + read_type = match.group(2).upper() + read_number = int(match.group(3)) + if read_type == 'I' and read_number == 1: + dt = SequencingFileType.I1 + elif read_type == 'I' and read_number == 2: + dt = SequencingFileType.I2 + elif read_type == 'R' and read_number == 1: + dt = SequencingFileType.R1 + elif read_type == 'R' and read_number == 2: + dt = SequencingFileType.R2 + elif read_type == 'R' and read_number == 3: + dt = SequencingFileType.R3 + elif read_type == 'R' and read_number == 4: + dt = SequencingFileType.R4 + else: + logger.warning('%s: Unrecognized read type: %s%d in %s.', run_id, read_type, read_number, filename) + break + detected_types.append(dt) + + if len(set(detected_types)) < len(detected_types): + logger.warning("%s: Non-unique sequencing file type detected: %s from %s.", run_id, detected_types, filenames) + return None + elif len(detected_types) == len(filenames): + return detected_types + else: + return None + +def detect_fallback_fastq_name(run_id, filenames): + """Fallback detection of sequencing file types based on very simplistic substring matching.""" + detected_types = [] + + # this is the most robust way of detecting file types + if len(detected_types) == len(filenames): + return detected_types + + # less robust detection, just lookup I1, I2, R1, R2 in filenames + for filename in filenames: + if 'I1' in filename: + detected_types.append(SequencingFileType.I1) + elif 'I2' in filename: + detected_types.append(SequencingFileType.I2) + elif 'R1' in filename: + detected_types.append(SequencingFileType.R1) + elif 'R2' in filename: + detected_types.append(SequencingFileType.R2) + elif 'R3' in filename: + detected_types.append(SequencingFileType.R3) + elif 'R4' in filename: + detected_types.append(SequencingFileType.R4) + else: + break + + if len(set(detected_types)) < len(detected_types): + logger.warning("%s: Non-unique sequencing file type detected: %s from %s.", run_id, detected_types, filenames) + return None + elif len(detected_types) == len(filenames): + return detected_types + else: + return None + +def order_layout_by_size_information(run_id: str, + layout: list[SequencingFileType], + file_sizes: Optional[list[int]], + read_lengths: Optional[list[float]]): + """ + Use information about file sizes and read lengths to guess the best order for a sequencing layout. + + This function essentially sorts the proposed layout in increasing order of read lengths (if available) or file size + (as a fallback). This is usually used to + """ + if read_lengths: + ix = [item[0] for item in sorted(enumerate(read_lengths), key=lambda item: item[1])] + return [layout[i] for i in ix] + elif file_sizes: + # this is less robust + ix = [item[0] for item in sorted(enumerate(file_sizes), key=lambda item: item[1])] + return [layout[i] for i in ix] + else: + raise ValueError( + f'Cannot infer the proper order for the FASTQ files of {run_id} since no read lengths nor file sizes information was provided.') diff --git a/rnaseq_pipeline/sources/arrayexpress.py b/rnaseq_pipeline/sources/arrayexpress.py index edb68df..65e0c4b 100644 --- a/rnaseq_pipeline/sources/arrayexpress.py +++ b/rnaseq_pipeline/sources/arrayexpress.py @@ -1,5 +1,7 @@ import os +from functools import lru_cache from os.path import join +from typing import List from urllib.request import urlretrieve import luigi @@ -9,12 +11,22 @@ from ..config import rnaseq_pipeline from ..platforms import IlluminaPlatform +from ..rnaseq_utils import detect_layout +from ..targets import DownloadRunTarget cfg = rnaseq_pipeline() +@lru_cache() +def retrieve_metadata(experiment_id): + # TODO: store metadata locally + metadata_url = f'https://www.ebi.ac.uk/arrayexpress/files/{experiment_id}/{experiment_id}.sdrf.txt' + ae_df = pd.read_csv(metadata_url, sep='\t') + ae_df = ae_df[ae_df['Comment[LIBRARY_STRATEGY]'] == 'RNA-Seq'] + return ae_df + class DownloadArrayExpressFastq(luigi.Task): - sample_id = luigi.Parameter() - fastq_url = luigi.Parameter() + sample_id: str = luigi.Parameter() + fastq_url: str = luigi.Parameter() resources = {'array_express_http_connections': 1} @@ -29,18 +41,47 @@ def output(self): return luigi.LocalTarget( join(cfg.OUTPUT_DIR, cfg.DATA, 'arrayexpress', self.sample_id, os.path.basename(self.fastq_url))) -class DownloadArrayExpressSample(TaskWithOutputMixin, WrapperTask): - experiment_id = luigi.Parameter() - sample_id = luigi.Parameter() - fastq_urls = luigi.ListParameter() +class DownloadArrayExpressRun(luigi.Task): + experiment_id: str = luigi.Parameter() + sample_id: str = luigi.Parameter() + run_id: str = luigi.Parameter() + fastq_filenames: List[str] = luigi.ListParameter() + fastq_urls: List[str] = luigi.ListParameter() @property def platform(self): + # TODO: detect platforms from ArrayExpress metadata return IlluminaPlatform('HiSeq 2500') + def run(self): + ae_df = retrieve_metadata(self.experiment_id) + run_metadata = ae_df[ae_df['ENA_RUN'] == self.run_id] + + yield [DownloadArrayExpressRun(experiment_id=self.experiment_id, sample_id=self.sample_id, run_id=run_id, + fastq_filenames=s['SUBMITTED_FILE_NAME'], fastq_urls=s['FASTQ_URI']) + for run_id, s in ae_df.groupby('Comment[ENA_RUN')] + def requires(self): return [DownloadArrayExpressFastq(self.sample_id, fastq_url) for fastq_url in self.fastq_urls] + def output(self): + return DownloadRunTarget(self.run_id, [i.path for i in self.input()], + detect_layout(self.run_id, self.fastq_filenames)) + +class DownloadArrayExpressSample(luigi.Task): + experiment_id = luigi.Parameter() + sample_id = luigi.Parameter() + + @property + def platform(self): + return IlluminaPlatform('HiSeq 2500') + + def run(self): + ae_df = retrieve_metadata(self.experiment_id) + sample_metadata = ae_df[ae_df['ENA_SAMPLE'] == self.sample_id] + yield [DownloadArrayExpressRun(experiment_id=self.experiment_id, sample_id=self.sample_id, run_id=run_id) + for run_id, s in sample_metadata.groupby('Comment[ENA_RUN]')] + class DownloadArrayExpressExperiment(TaskWithOutputMixin, WrapperTask): """ Download all the related ArrayExpress sample to this ArrayExpress experiment. @@ -48,11 +89,7 @@ class DownloadArrayExpressExperiment(TaskWithOutputMixin, WrapperTask): experiment_id = luigi.Parameter() def run(self): - # store metadata locally under metadata/arrayexpress/.sdrf.txt - ae_df = pd.read_csv('http://www.ebi.ac.uk/arrayexpress/files/{0}/{0}.sdrf.txt'.format(self.experiment_id), - sep='\t') - ae_df = ae_df[ae_df['Comment[LIBRARY_STRATEGY]'] == 'RNA-Seq'] + ae_df = retrieve_metadata(self.experiment_id) # FIXME: properly handle the order of paired FASTQs - yield [DownloadArrayExpressSample(experiment_id=self.experiment_id, sample_id=sample_id, - fastq_urls=s['Comment[FASTQ_URI]'].sort_values().tolist()) + yield [DownloadArrayExpressSample(experiment_id=self.experiment_id, sample_id=sample_id) for sample_id, s in ae_df.groupby('Comment[ENA_SAMPLE]')] diff --git a/rnaseq_pipeline/sources/gemma.py b/rnaseq_pipeline/sources/gemma.py index 47ebcfa..daa43f3 100644 --- a/rnaseq_pipeline/sources/gemma.py +++ b/rnaseq_pipeline/sources/gemma.py @@ -9,9 +9,12 @@ from .geo import DownloadGeoSample from .sra import DownloadSraExperiment +from ..config import rnaseq_pipeline from ..gemma import GemmaApi -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) + +cfg = rnaseq_pipeline() class DownloadGemmaExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ @@ -20,7 +23,7 @@ class DownloadGemmaExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): Gemma itself does not retain raw data, so this task delegates the work to other sources. """ - experiment_id = luigi.Parameter() + experiment_id: str = luigi.Parameter() def __init__(self, *kwargs, **kwds): super().__init__(*kwargs, **kwds) @@ -46,6 +49,8 @@ def run(self): @requires(DownloadGemmaExperiment) class ExtractGemmaExperimentBatchInfo(luigi.Task): + experiment_id: str + def run(self): with self.output().open('w') as info_out: for sample in self.requires().requires(): @@ -75,4 +80,4 @@ def run(self): info_out.write('\t'.join([sample.sample_id, fastq_id, platform_id, srx_uri, fastq_header]) + '\n') def output(self): - return luigi.LocalTarget(join(cfg.output_dir, 'fastq_headers', '{}.fastq-header'.format(self.experiment_id))) + return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'fastq_headers', '{}.fastq-header'.format(self.experiment_id))) diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py index aab6758..efb0c23 100644 --- a/rnaseq_pipeline/sources/geo.py +++ b/rnaseq_pipeline/sources/geo.py @@ -29,7 +29,7 @@ cfg = rnaseq_pipeline() -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) ns = {'miniml': 'http://www.ncbi.nlm.nih.gov/geo/info/MINiML'} @@ -64,7 +64,7 @@ class DownloadGeoSampleMetadata(TaskWithMetadataMixin, RerunnableTaskMixin, luig """ Download the MiNiML metadata for a given GEO Sample. """ - gsm = luigi.Parameter() + gsm: str = luigi.Parameter() resources = {'geo_http_connections': 1} @@ -91,6 +91,8 @@ class DownloadGeoSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ Download a GEO Sample given a runinfo file and """ + gsm: str + metadata: dict @property def sample_id(self): @@ -121,7 +123,7 @@ class DownloadGeoSeriesMetadata(TaskWithMetadataMixin, RerunnableTaskMixin, luig Download a GEO Series metadata containg information about related GEO Samples. """ - gse = luigi.Parameter() + gse: str = luigi.Parameter() resources = {'geo_http_connections': 1} @@ -131,7 +133,7 @@ def run(self): if self.output().is_stale(): logger.info('%s is stale, redownloading...', self.output()) res = requests.get('https://ftp.ncbi.nlm.nih.gov/geo/series/' + self.gse[ - :-3] + 'nnn/' + self.gse + '/miniml/' + self.gse + '_family.xml.tgz', + :-3] + 'nnn/' + self.gse + '/miniml/' + self.gse + '_family.xml.tgz', stream=True) res.raise_for_status() # we need to use a temporary file because Response.raw does not allow seeking @@ -154,6 +156,8 @@ class DownloadGeoSeries(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ Download all GEO Samples related to a GEO Series. """ + gse: str + metadata: dict ignored_samples = luigi.ListParameter(default=[], description='Ignored GSM identifiers') @@ -170,6 +174,7 @@ class ExtractGeoSeriesBatchInfo(luigi.Task): Extract the GEO Series batch information by looking up the GEO Series metadata and some downloaded FASTQs headers. """ + gse: str def run(self): geo_series_metadata, samples = self.requires() diff --git a/rnaseq_pipeline/sources/local.py b/rnaseq_pipeline/sources/local.py index 1588ac3..63c7a83 100644 --- a/rnaseq_pipeline/sources/local.py +++ b/rnaseq_pipeline/sources/local.py @@ -6,6 +6,7 @@ from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask from ..config import rnaseq_pipeline +from ..platforms import IlluminaPlatform cfg = rnaseq_pipeline() @@ -14,8 +15,8 @@ class DownloadLocalSample(luigi.Task): Local samples are organized by :experiment_id: to avoid name clashes across experiments. """ - experiment_id = luigi.Parameter() - sample_id = luigi.Parameter() + experiment_id: str = luigi.Parameter() + sample_id: str = luigi.Parameter() @property def platform(self): @@ -27,7 +28,7 @@ def output(self): sorted(glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, self.sample_id, '*.fastq.gz')))] class DownloadLocalExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): - experiment_id = luigi.Parameter() + experiment_id: str = luigi.Parameter() def run(self): yield [DownloadLocalSample(self.experiment_id, os.path.basename(f)) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 295ea17..b193210 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -1,30 +1,50 @@ +""" +This module contains all the logic to retrieve RNA-Seq data from SRA. +""" +import enum import gzip import logging import os import subprocess import xml.etree.ElementTree as ET +from dataclasses import dataclass from datetime import timedelta from os.path import join -from subprocess import Popen, check_output, PIPE +from typing import Optional, List import luigi import pandas as pd from bioluigi.tasks import sratoolkit -from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask, TaskWithMetadataMixin +from bioluigi.tasks.utils import TaskWithMetadataMixin, DynamicTaskWithOutputMixin, DynamicWrapperTask from luigi.util import requires from ..config import rnaseq_pipeline from ..platforms import IlluminaPlatform -from ..targets import ExpirableLocalTarget +from ..rnaseq_utils import SequencingFileType, detect_layout +from ..targets import ExpirableLocalTarget, DownloadRunTarget from ..utils import remove_task_output, RerunnableTaskMixin cfg = rnaseq_pipeline() -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) + +class sra(luigi.Config): + task_namespace = 'rnaseq_pipeline.sources' + ncbi_public_dir: str = luigi.Parameter() + +sra_config = sra() + +# columns to use when a runinfo file lacks a header +SRA_RUNINFO_COLUMNS = ['Run', 'ReleaseDate', 'LoadDate', 'spots', 'bases', 'spots_with_mates', 'avgLength', 'size_MB', + 'AssemblyName', 'download_path', 'Experiment', 'LibraryName', 'LibraryStrategy', + 'LibrarySelection', 'LibrarySource', 'LibraryLayout', 'InsertSize', 'InsertDev', 'Platform', + 'Model', 'SRAStudy', 'BioProject', 'Study_Pubmed_id', 'ProjectID', 'Sample', 'BioSample', + 'SampleType', 'TaxID', 'ScientificName', 'SampleName', 'g1k_pop_code', 'source', + 'g1k_analysis_group', 'Subject_ID', 'Sex', 'Disease', 'Tumor', 'Affection_Status', + 'Analyte_Type', 'Histological_Type', 'Body_Site', 'CenterName', 'Submission', + 'dbgap_study_accession', 'Consent', 'RunHash', 'ReadHash'] def read_runinfo(path): - SRA_RUNINFO_COLUMNS = 'Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash'.split( - ',') df = pd.read_csv(path) if df.columns[0] != 'Run': logger.warning('Runinfo file %s is missing a header, a fallback will be used instead.', path) @@ -32,9 +52,218 @@ def read_runinfo(path): df = pd.read_csv(path, names=SRA_RUNINFO_COLUMNS[:len(df.columns)]) return df -""" -This module contains all the logic to retrieve RNA-Seq data from SRA. -""" +class SraRunIssue(enum.IntFlag): + """Issues that can occur when processing SRA runs.""" + NO_SRA_FILES = enum.auto() + NO_SPOT_STATISTICS = enum.auto() + NO_FASTQ_LOAD = enum.auto() + NO_FASTQ_LOAD_OPTIONS = enum.auto() + MISMATCHED_FASTQ_LOAD_OPTIONS = enum.auto() + AMBIGUOUS_READ_SIZES = enum.auto() + MISMATCHED_READ_SIZES = enum.auto() + INVALID_RUN = enum.auto() + +@dataclass +class SraRunMetadata: + """A digested SRA run metadata""" + srx: str + srr: str + is_paired: bool + fastq_filenames: list[str] + fastq_file_sizes: list[int] + # only available if statistics were present in the XML metadata + number_of_spots: Optional[int] + average_read_lengths: Optional[list[float]] + fastq_load_options: Optional[dict] + layout: list[SequencingFileType] + issues: SraRunIssue + +def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: + """ + :param path: Path to the XML file containing SRA run metadata. + :param include_invalid_runs: If True, include runs that do not have any suitable metadata that can be used to + determine the layout. + :return: + """ + root = ET.parse(path) + runs = root.findall('EXPERIMENT_PACKAGE/RUN_SET/RUN') + result = [] + for run in runs: + srr = run.attrib['accession'] + + srx = run.find('EXPERIMENT_REF').attrib['accession'] + is_single_end = root.find( + 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/SINGLE') is not None + is_paired = root.find( + 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/PAIRED') is not None + + sra_files = run.findall('SRAFiles/SRAFile[@semantic_name=\'fastq\']') + + issues = SraRunIssue(0) + + if not sra_files: + issues |= SraRunIssue.NO_SRA_FILES + + # if the data was loaded with fastq-load.py, we can obtain the order of the files from the options + loader, options = None, None + run_attributes = run.findall('RUN_ATTRIBUTES/RUN_ATTRIBUTE') + for run_attribute in run_attributes: + tag, value = run_attribute.find('TAG'), run_attribute.find('VALUE') + if tag.text == 'loader': + loader = value.text + elif tag.text == 'options': + options = value.text + options = {k: v for k, v in + (o.split('=', maxsplit=1) if '=' in o else (o, None) for o in options.split())} + + if loader == 'fastq-load.py': + # parse options... + # TODO: use argparse or something safer + fastq_load_files = [] + if options: + opts = ['--read1PairFiles', + '--read2PairFiles', + '--read3PairFiles', + '--read4PairFiles'] + for o in opts: + if o in options: + fastq_load_files.append(options[o]) + else: + logger.warning('%s: The fastq-load.py loader does not have any option.', srr) + fastq_load_files = None + issues |= SraRunIssue.NO_FASTQ_LOAD_OPTIONS + else: + issues |= SraRunIssue.NO_FASTQ_LOAD + fastq_load_files = None + + statistics = run.find('Statistics') + if statistics: + number_of_spots = int(statistics.attrib['nreads']) + reads = sorted(statistics.findall('Read'), key=lambda r: int(r.attrib['index'])) + spot_read_lengths = [float(r.attrib['average']) for r in reads] + else: + logger.warning( + '%s: No spot statistics found, cannot use the average read lengths to determine the order of the FASTQ files.', + srr) + number_of_spots = None + reads = None + spot_read_lengths = None + issues |= SraRunIssue.NO_SPOT_STATISTICS + + # sort the SRA files to match the spots using fastq-load.py options + if loader == 'fastq-load.py' and fastq_load_files: + + if set(fastq_load_files) == set([sf.attrib['filename'] for sf in sra_files]): + logger.info('%s: Using the arguments passed to fastq-load.py to reorder the SRA files.', srr) + sra_files = sorted(sra_files, key=lambda f: fastq_load_files.index(f.attrib['filename'])) + fastq_filenames = [sf.attrib['filename'] for sf in sra_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + + # try to add a .gz suffix to the SRA files + elif set(fastq_load_files) == set([sf.attrib['filename'] + '.gz' for sf in sra_files]): + logger.warning( + '%s: The SRA files lack .gz extensions: %s, but still correspond to fastq-load.py options: %s, will use those to reorder the SRA files.', + srx, [sf.attrib['filename'] for sf in sra_files], fastq_load_files) + sra_files = sorted(sra_files, + key=lambda f: fastq_load_files.index(f.attrib['filename'] + '.gz')) + fastq_filenames = [sf.attrib['filename'] for sf in sra_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + + elif sra_files: + logging.warning( + "%s: The SRA files: %s do not match arguments passed to fastq-load.py: %s. The filenames passed to fastq-load.py will be used instead: %s.", + srr, + [sf.attrib['filename'] for sf in sra_files], + options, + fastq_load_files) + fastq_filenames = fastq_load_files + fastq_file_sizes = None + issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS + + else: + logging.warning( + "%s: No SRA files found, but the arguments of fastq-load.py are present: %s. The filenames passed to fastq-load.py will be used: %s.", + srr, options, fastq_load_files) + fastq_filenames = fastq_load_files + fastq_file_sizes = None + + # use spot statistics to determine the order of the files by matching their sizes with the sizes of the files + # this is less reliable than using the fastq-load.py options, but it is still better than nothing + # we can only use this strategy if all the read sizes are different and can be related to the file sizes + elif statistics: + # check if the sizes are unambiguous? + read_sizes = [int(read.attrib['count']) * float(read.attrib['average']) for read in reads] + if len(set(read_sizes)) == len(read_sizes): + # sort the files according to the layout + # sort the layout according to the average read size + reads_by_size = [e[0] for e in sorted(enumerate(reads), + key=lambda e: int(e[1].attrib['count']) * float( + e[1].attrib['average']))] + files_by_size = [e[0] for e in sorted(enumerate(sra_files), key=lambda e: int(e[1].attrib['size']))] + + if len(reads_by_size) == len(files_by_size): + if reads_by_size != files_by_size: + logger.info('%s: Reordering SRA files to match the read sizes in the spot...', srr) + sra_files = [sra_files[reads_by_size.index(files_by_size[i])] for i, sra_file in + enumerate(sra_files)] + fastq_filenames = [sf.attrib['filename'] for sf in sra_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + else: + # shot + logger.warning( + '%s: The number of reads: %d and files: %d do not correspond, cannot use them to order SRA files by filesize. Only the spot metadata will be used to determine the layout.', + srr, len(reads_by_size), len(files_by_size)) + fastq_filenames = None + fastq_file_sizes = None + issues |= SraRunIssue.MISMATCHED_READ_SIZES + else: + # this is extremely common, so it's not worth warning about it + logger.info( + '%s: Number of bps per read are ambiguous: %s, cannot use them to order SRA files by filesize. Only the spot metadata will be used to determine the layout.', + srr, read_sizes) + fastq_filenames = None + fastq_file_sizes = None + issues |= SraRunIssue.AMBIGUOUS_READ_SIZES + + else: + issues |= SraRunIssue.INVALID_RUN + logger.warning( + '%s: No information found that can be used to order SRA files, ignoring that run.', + srr) + if include_invalid_runs: + fastq_filenames = [sf.attrib['filename'] for sf in sra_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + result.append(SraRunMetadata(srx, srr, + is_paired=is_paired, + fastq_filenames=fastq_filenames, + fastq_file_sizes=fastq_file_sizes, + number_of_spots=None, + average_read_lengths=None, + fastq_load_options=None, + layout=[], + issues=issues)) + continue + + try: + layout = detect_layout(srr, fastq_filenames, fastq_file_sizes, spot_read_lengths, is_single_end, is_paired) + except ValueError: + logger.warning('%s: Failed to detect layout, ignoring that run.', srr, exc_info=True) + if include_invalid_runs: + layout = [] + issues |= SraRunIssue.INVALID_RUN + else: + continue + + result.append(SraRunMetadata(srx, srr, + is_paired=is_paired, + fastq_filenames=fastq_filenames, + fastq_file_sizes=fastq_file_sizes, + number_of_spots=number_of_spots, + average_read_lengths=spot_read_lengths, + fastq_load_options=options if loader == 'fastq-load.py' else None, + layout=layout, + issues=issues)) + return result class PrefetchSraRun(TaskWithMetadataMixin, luigi.Task): """ @@ -42,35 +271,33 @@ class PrefetchSraRun(TaskWithMetadataMixin, luigi.Task): SRA archives are stored in a shared cache. """ - srr = luigi.Parameter(description='SRA run identifier') + srr: str = luigi.Parameter(description='SRA run identifier') retry_count = 3 - @staticmethod - def _get_ncbi_public_dir(): - ret = subprocess.run(['vdb-config', '-p'], stdout=subprocess.PIPE, universal_newlines=True) - config_xml = ET.fromstring(ret.stdout) - return config_xml.find('repository').find('user').find('main').find('public').find('root').text - def run(self): - yield sratoolkit.Prefetch(self.srr, - self.output().path, + yield sratoolkit.Prefetch(srr_accession=self.srr, + output_file=self.output().path, max_size=100, scheduler_partition='Wormhole', metadata=self.metadata, walltime=timedelta(hours=2)) def output(self): - return luigi.LocalTarget(join(self._get_ncbi_public_dir(), 'sra', f'{self.srr}.sra')) + return luigi.LocalTarget(join(sra_config.ncbi_public_dir, 'sra', f'{self.srr}.sra')) @requires(PrefetchSraRun) class DumpSraRun(luigi.Task): """ Dump FASTQs from a SRA run archive """ - srx = luigi.Parameter(description='SRA experiment identifier') + srx: str = luigi.Parameter(description='SRA experiment identifier') + srr: str + + layout: list[str] = luigi.ListParameter(positional=False, + description='Indicate the type of each output file from the run. Possible values are I1, I2, R1 and R2.') - paired_reads = luigi.BoolParameter(positional=False, description='Indicate of reads have paired or single mates') + metadata: dict def on_success(self): # cleanup SRA archive once dumped if it's still hanging around @@ -79,32 +306,41 @@ def on_success(self): return super().on_success() def run(self): - yield sratoolkit.FastqDump(self.input().path, - join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), + yield sratoolkit.FastqDump(input_file=self.input().path, + output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), + split='files', + number_of_reads_per_spot=len(self.layout), metadata=self.metadata) if not self.complete(): - labelling = 'paired' if self.paired_reads else 'single-end' raise RuntimeError( - f'{repr(self)} was not completed after successful fastq-dump execution. Is it possible the SRA run is mislabelled as {labelling}?') + f'{repr(self)} was not completed after successful fastq-dump execution; are the output files respecting the following layout: {self.layout}?') def output(self): output_dir = join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx) - if self.paired_reads: - return [luigi.LocalTarget(join(output_dir, self.srr + '_1.fastq.gz')), - luigi.LocalTarget(join(output_dir, self.srr + '_2.fastq.gz'))] - return [luigi.LocalTarget(join(output_dir, self.srr + '.fastq.gz'))] + expected_files = len(self.layout) + if expected_files > 1: + return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '_' + str(i) + '.fastq.gz') for i in + range(1, expected_files + 1)], self.layout) + return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '.fastq.gz')], self.layout) class EmptyRunInfoError(Exception): pass -def retrieve_runinfo(sra_accession): +def retrieve_sra_metadata(sra_accession, format='runinfo'): """Retrieve a SRA runinfo using search and efetch utilities""" - runinfo_data = check_output(['efetch', '-db', 'sra', '-id', sra_accession, '-format', 'runinfo'], universal_newlines=True) - if not runinfo_data.strip() or (len(runinfo_data.splitlines()) == 1 and runinfo_data[:3] == 'Run'): + if isinstance(sra_accession, str): + p = subprocess.run(['efetch', '-db', 'sra', '-id', sra_accession, '-format', format], + text=True, stdout=subprocess.PIPE, check=True) + else: + logger.info('Passing ' + str(len(sra_accession)) + ' SRX accessions to efetch...') + p = subprocess.run(['efetch', '-db', 'sra', '-format', format], input='\n'.join(sra_accession), + text=True, stdout=subprocess.PIPE, check=True) + runinfo_data = p.stdout.strip() + if format == 'runinfo' and not runinfo_data or (len(runinfo_data.splitlines()) == 1 and runinfo_data[:3] == 'Run'): raise EmptyRunInfoError(f"Runinfo for {sra_accession} is empty.") return runinfo_data -class DownloadSraExperimentRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task): +class DownloadSraExperimentMetadata(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task): srx = luigi.Parameter(description='SRX accession to use') resources = {'edirect_http_connections': 1} @@ -116,13 +352,13 @@ def run(self): if self.output().is_stale(): logger.info('%s is stale, redownloading...', self.output()) with self.output().open('w') as f: - f.write(retrieve_runinfo(self.srx)) + f.write(retrieve_sra_metadata(self.srx, format='xml')) def output(self): - return ExpirableLocalTarget(join(cfg.OUTPUT_DIR, cfg.METADATA, 'sra', '{}.runinfo'.format(self.srx)), + return ExpirableLocalTarget(join(cfg.OUTPUT_DIR, cfg.METADATA, 'sra', '{}.xml'.format(self.srx)), ttl=timedelta(days=14)) -@requires(DownloadSraExperimentRunInfo) +@requires(DownloadSraExperimentMetadata) class DownloadSraExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ Download a SRA experiment comprising one SRA run @@ -131,12 +367,12 @@ class DownloadSraExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): associated runs. The default is to select the latest run based on the lexicographic order of its identifier. """ - srr = luigi.OptionalParameter(default=None, description='Specific SRA run accession to use (defaults to latest)') + srx: str + srr = luigi.OptionalListParameter(default=None, description='Specific SRA run accessions to use (defaults to all)') + + metadata: dict - force_single_end = luigi.BoolParameter(positional=False, significant=False, default=False, - description='Force the library layout to be single-end') - force_paired_reads = luigi.BoolParameter(positional=False, significant=False, default=False, - description='Force the library layout to be paired') + unpack_singleton = False @property def sample_id(self): @@ -147,32 +383,27 @@ def platform(self): return IlluminaPlatform('HiSeq 2500') def run(self): - # this will raise an error of no FASTQs are related - df = read_runinfo(self.input().path) + meta = read_xml_metadata(self.input().path) if self.srr is not None: - run = df[df.Run == self.srr].iloc[0] - else: - run = df.sort_values('Run', ascending=False).iloc[0] + meta = [r for r in meta if r.srr in self.srr] - if self.force_paired_reads: - is_paired = True - elif self.force_single_end: - is_paired = False - else: - is_paired = run.LibraryLayout == 'PAIRED' + if not meta: + raise ValueError(f'No SRA runs found for {self.srx}.') metadata = dict(self.metadata) # do not override the sample_id when invoked from DownloadGeoSample or DownloadGemmaExperiment if 'sample_id' not in metadata: metadata['sample_id'] = self.sample_id - yield DumpSraRun(run.Run, self.srx, paired_reads=is_paired, metadata=metadata) + + for row in meta: + yield DumpSraRun(srr=row.srr, srx=self.srx, layout=[ft.name for ft in row.layout], metadata=metadata) class DownloadSraProjectRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task): """ Download a SRA project """ - srp = luigi.Parameter(description='SRA project identifier') + srp: str = luigi.Parameter(description='SRA project identifier') resources = {'edirect_http_connections': 1} @@ -181,7 +412,7 @@ class DownloadSraProjectRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luig def run(self): with self.output().open('w') as f: - f.write(retrieve_runinfo(self.srp)) + f.write(retrieve_sra_metadata(self.srp, format='runinfo')) def output(self): return ExpirableLocalTarget(join(cfg.OUTPUT_DIR, cfg.METADATA, 'sra', '{}.runinfo'.format(self.srp)), @@ -190,6 +421,7 @@ def output(self): @requires(DownloadSraProjectRunInfo) class DownloadSraProject(DynamicTaskWithOutputMixin, DynamicWrapperTask): ignored_samples = luigi.ListParameter(default=[], description='Ignored SRX identifiers') + metadata: dict def run(self): df = read_runinfo(self.input().path) @@ -202,6 +434,8 @@ class ExtractSraProjectBatchInfo(luigi.Task): Extract the batch information for a given SRA project. """ + srp: str + def run(self): run_info, samples = self.input() with self.output().open('w') as info_out: diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index 8900805..0921f6e 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -84,3 +84,21 @@ def is_stale(self): def exists(self): return super().exists() and not self.is_stale() + +class DownloadRunTarget(luigi.Target): + run_id: str + files: list[str] + layout: list[str] + + _targets: list[luigi.LocalTarget] + + def __init__(self, run_id, files, layout): + if len(files) != len(layout): + raise ValueError('The number of files must match the layout.') + self.run_id = run_id + self.files = files + self.layout = layout + self._targets = [luigi.LocalTarget(f) for f in files] + + def exists(self): + return all(t.exists() for t in self._targets) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index c86b3b4..11c0ffa 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -12,6 +12,7 @@ import requests from bioluigi.scheduled_external_program import ScheduledExternalProgramTask from bioluigi.tasks import fastqc, multiqc +from bioluigi.tasks.cellranger import CellRangerCount from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, TaskWithOutputMixin, DynamicWrapperTask from luigi.task import flatten_output, WrapperTask from luigi.util import requires @@ -26,7 +27,7 @@ from .targets import GemmaDatasetPlatform, GemmaDatasetHasBatch, RsemReference from .utils import no_retry, RerunnableTaskMixin, remove_task_output -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) cfg = rnaseq_pipeline() gemma_cfg = gemma() @@ -37,9 +38,15 @@ class DownloadSample(TaskWithOutputMixin, WrapperTask): experiment. Note that the 'gemma' source does not provide individual samples. + + The output of this task is a list of tuple of FASTQ files organized as follows: + - for single-end reads, [(R1)] + - for paired-end reads, [(R1, R2)] + - for paired-end reads with an index file, [(I1, R1, R2)] + - for paired-end reads with two index files, [(I1, I2, R1, R2)] """ - experiment_id = luigi.Parameter() - sample_id = luigi.Parameter() + experiment_id: str = luigi.Parameter() + sample_id: str = luigi.Parameter() source = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'arrayexpress', 'local', 'sra'], positional=False) @@ -93,6 +100,8 @@ class TrimSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): :attr ignore_mate: Ignore either the forward or reverse mate in the case of paired reads, defaults to neither. """ + experiment_id: str + sample_id: str ignore_mate = luigi.ChoiceParameter(choices=['forward', 'reverse', 'neither'], default='neither', positional=False) minimum_length = luigi.IntParameter(default=25, positional=False) @@ -163,11 +172,13 @@ class QualityControlSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ Perform post-download quality control on the FASTQs. """ + experiment_id: str + sample_id: str def run(self): destdir = join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id, self.sample_id) os.makedirs(destdir, exist_ok=True) - yield [fastqc.GenerateReport(fastq_in.path, destdir, temp_dir=tempfile.gettempdir()) for fastq_in in + yield [fastqc.GenerateReport(fastq_in.path, output_dir=destdir, temp_dir=tempfile.gettempdir()) for fastq_in in self.input()] class QualityControlExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): @@ -196,8 +207,8 @@ class PrepareReference(ScheduledExternalProgramTask): :param taxon: Taxon :param reference_id: Reference annotation build to use (i.e. ensembl98, hg38_ncbi) """ - taxon = luigi.Parameter() - reference_id = luigi.Parameter() + taxon: str = luigi.Parameter() + reference_id: str = luigi.Parameter() cpus = 16 memory = 32 @@ -246,6 +257,10 @@ class AlignSample(ScheduledExternalProgramTask): :attr strand_specific: Indicate if the RNA-Seq data is stranded """ + reference_id: str + experiment_id: str + sample_id: str + # TODO: handle strand-specific reads strand_specific = luigi.BoolParameter(default=False, positional=False) @@ -279,17 +294,32 @@ def program_args(self): if self.strand_specific: args.append('--strand-specific') - sample_run, reference = self.input() + runs, reference = self.input() + + forward_reads = [] + reverse_reads = [] + for run in runs: + if 'R1' in run.layout and 'R2' in run.layout: + forward_reads.append(run.files[run.layout.index('R1')]) + reverse_reads.append(run.files[run.layout.index('R2')]) + elif 'R1' in run.layout: + forward_reads.append(run.files[run.layout.index('R1')]) + elif 'R2' in run.layout: + logging.warning('Found an unpaired reverse read in run %s, will treat it as single-end.', run.run_id) + forward_reads.append(run.files[run.layout.index('R1')]) + else: + logger.warning("Unsupported layout for run %s, it will be ignored.", run.run_id) + + if not forward_reads: + raise ValueError('No forward reads found in the input runs. Please check the input data.') - fastqs = [mate.path for mate in sample_run] + args.append(','.join(forward_reads)) - if len(fastqs) == 1: - args.append(fastqs[0]) - elif len(fastqs) == 2: + if reverse_reads: + if len(forward_reads) != len(reverse_reads): + raise ValueError('If reverse reads are provided, they must match the number of forward reads.') args.append('--paired-end') - args.extend(fastqs) - else: - raise NotImplementedError('Alignment of more than two input FASTQs is not supported.') + args.append(','.join(reverse_reads)) # reference for alignments and quantifications args.append(reference.prefix) @@ -309,20 +339,20 @@ class AlignExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): The output is one sample alignment output per sample contained in the experiment. """ - experiment_id = luigi.Parameter() - source = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'sra', 'arrayexpress', 'local'], - positional=False) - taxon = luigi.Parameter(positional=False) - reference_id = luigi.Parameter(positional=False) - scope = luigi.Parameter(default='genes', positional=False) + experiment_id: str = luigi.Parameter() + source: str = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'sra', 'arrayexpress', 'local'], + positional=False) + taxon: str = luigi.Parameter(positional=False) + reference_id: str = luigi.Parameter(positional=False) + scope: str = luigi.Parameter(default='genes', positional=False) def requires(self): return DownloadExperiment(self.experiment_id, source=self.source).requires().requires() def run(self): download_sample_tasks = next(DownloadExperiment(self.experiment_id, source=self.source).requires().run()) - yield [AlignSample(self.experiment_id, - dst.sample_id, + yield [AlignSample(experiment_id=self.experiment_id, + sample_id=dst.sample_id, source=self.source, taxon=self.taxon, reference_id=self.reference_id, @@ -337,6 +367,8 @@ class GenerateReportForExperiment(RerunnableTaskMixin, luigi.Task): The report include collected FastQC reports and RSEM/STAR outputs. """ + experiment_id: str + reference_id: str def run(self): fastqc_dir = join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id) @@ -366,7 +398,9 @@ def run(self): sample_id += '_2' out.write(f'{fastqc_sample_id}\t{sample_id}\n') - yield multiqc.GenerateReport(search_dirs, dirname(self.output().path), replace_names=sample_names_file, + yield multiqc.GenerateReport(input_dirs=search_dirs, + output_dir=dirname(self.output().path), + replace_names=sample_names_file, force=self.rerun) def output(self): @@ -381,6 +415,10 @@ class CountExperiment(luigi.Task): The output is constituted of two matrices: genes counts and FPKM. """ + reference_id: str + experiment_id: str + scope: str + resources = {'cpus': 1} def run(self): @@ -402,6 +440,70 @@ def output(self): return [luigi.LocalTarget(join(destdir, f'{self.experiment_id}_counts.{self.scope}')), luigi.LocalTarget(join(destdir, f'{self.experiment_id}_fpkm.{self.scope}'))] +class PrepareSingleCellReference(luigi.Task): + reference_id = luigi.Parameter() + + def output(self): + return luigi.LocalTarget( + join(str(cfg.OUTPUT_DIR), str(cfg.SINGLE_CELL_REFERENCES), str(self.reference_id))) + +@requires(DownloadSample) +class OrganizeSingleCellSample(luigi.Task): + """Pre-populate a directory with FASTQs for a single-cell sample""" + + experiment_id: str + sample_id: str + + def run(self): + runs = self.input() + os.makedirs(self.output().path) + for lane, run in enumerate(runs): + for f, read_type in zip(run.files, run.layout): + dest = join(self.output().path, f'{self.sample_id}_S1_L{lane + 1:03}_{read_type}_001.fastq.gz') + if os.path.exists(dest): + os.unlink(dest) + os.link(f, dest) + + def output(self): + return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'data-single-cell', self.experiment_id, self.sample_id)) + +@requires(OrganizeSingleCellSample, PrepareSingleCellReference) +class AlignSingleCellSample(DynamicWrapperTask): + experiment_id: str + sample_id: str + + def run(self): + fastqs_dir, transcriptome_dir = self.input() + yield CellRangerCount( + id=self.sample_id, + transcriptome_dir=transcriptome_dir, + fastqs_dir=fastqs_dir, + output_dir=self.output().path, + # TODO: add an avx feature on slurm + scheduler_extra_args=['--constraint', 'thrd64'] + ) + + def output(self): + return luigi.LocalTarget( + join(cfg.OUTPUT_DIR, 'quantified-single-cell', self.reference_id, self.experiment_id, self.sample_id)) + +class AlignSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): + experiment_id: str = luigi.Parameter() + source: str = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'sra', 'arrayexpress', 'local'], + positional=False) + reference_id: str = luigi.Parameter(positional=False) + + def requires(self): + return DownloadExperiment(self.experiment_id, source=self.source).requires().requires() + + def run(self): + download_sample_tasks = next(DownloadExperiment(self.experiment_id, source=self.source).requires().run()) + yield [AlignSingleCellSample(experiment_id=self.experiment_id, + sample_id=dst.sample_id, + source=self.source, + reference_id=self.reference_id) + for dst in download_sample_tasks] + class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaCliTask): """ Submit the batch information of an experiment to Gemma. @@ -465,7 +567,7 @@ class SubmitExperimentReportToGemma(RerunnableTaskMixin, GemmaCliTask): """ Submit an experiment QC report to Gemma. """ - experiment_id = luigi.Parameter() + experiment_id: str = luigi.Parameter() subcommand = 'addMetadataFile' @@ -484,6 +586,24 @@ def output(self): return luigi.LocalTarget( join(gemma_cfg.appdata_dir, 'metadata', self.experiment_id, 'MultiQCReports/multiqc_report.html')) +class SubmitSingleCellExperimentDataToGemma(RerunnableTaskMixin, GemmaCliTask): + experiment_id: str = luigi.Parameter() + subcommand = 'loadSingleCellData' + + def requires(self): + return AlignSingleCellExperiment(experiment_id=self.experiment_id, + reference_id=self.single_cell_reference_id(), + source='gemma') + + def subcommand_args(self): + return ['-e', self.experiment_id, '-a', self.platform_short_name, + '--data-path', self.input().path, + '--quantitation-type-recomputed-from-raw-data', + '--preferred-quantitation-type', + # TODO: add sequencing metadata + # FIXME: add --replace + ] + @requires(SubmitExperimentDataToGemma, SubmitExperimentBatchInfoToGemma, SubmitExperimentReportToGemma) class SubmitExperimentToGemma(TaskWithOutputMixin, WrapperTask): """ @@ -491,6 +611,7 @@ class SubmitExperimentToGemma(TaskWithOutputMixin, WrapperTask): TODO: add QC report submission """ + experiment_id: str # Makes it so that we recheck if the task is complete after 20 minutes. # This is because Gemma Web API is caching reply for 1200 seconds, so the @@ -552,8 +673,14 @@ def requires(self): except AttributeError as e: raise Exception(f'Failed to read experiments from {self._filename()}, is it valid?') from e + def _filename(self): + raise NotImplementedError + + def _retrieve_dataframe(self): + raise NotImplementedError + class SubmitExperimentsFromFileToGemma(SubmitExperimentsFromDataFrameMixin, TaskWithOutputMixin, WrapperTask): - input_file = luigi.Parameter() + input_file: str = luigi.Parameter() def _filename(self): return self.input_file @@ -562,9 +689,9 @@ def _retrieve_dataframe(self): return pd.read_csv(self.input_file, sep='\t', converters={'priority': lambda x: 0 if x == '' else int(x)}) class SubmitExperimentsFromGoogleSpreadsheetToGemma(SubmitExperimentsFromDataFrameMixin, WrapperTask): - spreadsheet_id = luigi.Parameter( + spreadsheet_id: str = luigi.Parameter( description='Spreadsheet ID in Google Sheets (lookup {spreadsheetId} in https://docs.google.com/spreadsheets/d/{spreadsheetId}/edit)') - sheet_name = luigi.Parameter(description='Name of the spreadsheet in the document') + sheet_name: str = luigi.Parameter(description='Name of the spreadsheet in the document') def _filename(self): return 'https://docs.google.com/spreadsheets/d/' + self.spreadsheet_id diff --git a/rnaseq_pipeline/utils.py b/rnaseq_pipeline/utils.py index 4a67368..d32e86a 100644 --- a/rnaseq_pipeline/utils.py +++ b/rnaseq_pipeline/utils.py @@ -3,7 +3,7 @@ import luigi from luigi.task import flatten_output -logger = logging.getLogger('luigi-interface') +logger = logging.getLogger(__name__) class IlluminaFastqHeader: @classmethod diff --git a/rnaseq_pipeline/webviewer/__init__.py b/rnaseq_pipeline/webviewer/__init__.py index 3d92fc0..2c972f5 100644 --- a/rnaseq_pipeline/webviewer/__init__.py +++ b/rnaseq_pipeline/webviewer/__init__.py @@ -1,4 +1,3 @@ -from os.path import basename, getctime, join, dirname import datetime from glob import glob from os.path import basename, getctime, join, dirname diff --git a/tests/data/GSE104493.xml b/tests/data/GSE104493.xml new file mode 100644 index 0000000..0abac7e --- /dev/null +++ b/tests/data/GSE104493.xml @@ -0,0 +1,133041 @@ + + + + + + + SRX3237802 + + GSM2802435: U87 scRNA-Seq U87_SC_h9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561528 + GSM2802435 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802435 + + + + + + + GEO Accession + GSM2802435 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561528 + SAMN07729919 + GSM2802435 + + U87 scRNA-Seq U87_SC_h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561528 + SAMN07729919 + GSM2802435 + + + + + + + SRR6125149 + GSM2802435_r1 + + + + + + SRS2561528 + SAMN07729919 + GSM2802435 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237801 + + GSM2802434: U87 scRNA-Seq U87_SC_h8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561527 + GSM2802434 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802434 + + + + + + + GEO Accession + GSM2802434 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561527 + SAMN07729920 + GSM2802434 + + U87 scRNA-Seq U87_SC_h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561527 + SAMN07729920 + GSM2802434 + + + + + + + SRR6125148 + GSM2802434_r1 + + + + + + SRS2561527 + SAMN07729920 + GSM2802434 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237800 + + GSM2802433: U87 scRNA-Seq U87_SC_h7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561525 + GSM2802433 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802433 + + + + + + + GEO Accession + GSM2802433 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561525 + SAMN07729921 + GSM2802433 + + U87 scRNA-Seq U87_SC_h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561525 + SAMN07729921 + GSM2802433 + + + + + + + SRR6125147 + GSM2802433_r1 + + + + + + SRS2561525 + SAMN07729921 + GSM2802433 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237799 + + GSM2802432: U87 scRNA-Seq U87_SC_h6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561526 + GSM2802432 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802432 + + + + + + + GEO Accession + GSM2802432 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561526 + SAMN07729922 + GSM2802432 + + U87 scRNA-Seq U87_SC_h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561526 + SAMN07729922 + GSM2802432 + + + + + + + SRR6125146 + GSM2802432_r1 + + + + + + SRS2561526 + SAMN07729922 + GSM2802432 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237798 + + GSM2802431: U87 scRNA-Seq U87_SC_h5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561524 + GSM2802431 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802431 + + + + + + + GEO Accession + GSM2802431 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561524 + SAMN07729923 + GSM2802431 + + U87 scRNA-Seq U87_SC_h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561524 + SAMN07729923 + GSM2802431 + + + + + + + SRR6125145 + GSM2802431_r1 + + + + + + SRS2561524 + SAMN07729923 + GSM2802431 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237797 + + GSM2802430: U87 scRNA-Seq U87_SC_h4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561523 + GSM2802430 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802430 + + + + + + + GEO Accession + GSM2802430 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561523 + SAMN07729924 + GSM2802430 + + U87 scRNA-Seq U87_SC_h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561523 + SAMN07729924 + GSM2802430 + + + + + + + SRR6125144 + GSM2802430_r1 + + + + + + SRS2561523 + SAMN07729924 + GSM2802430 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237796 + + GSM2802429: U87 scRNA-Seq U87_SC_h3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561522 + GSM2802429 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802429 + + + + + + + GEO Accession + GSM2802429 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561522 + SAMN07729925 + GSM2802429 + + U87 scRNA-Seq U87_SC_h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561522 + SAMN07729925 + GSM2802429 + + + + + + + SRR6125143 + GSM2802429_r1 + + + + + + SRS2561522 + SAMN07729925 + GSM2802429 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237795 + + GSM2802428: U87 scRNA-Seq U87_SC_h2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561521 + GSM2802428 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802428 + + + + + + + GEO Accession + GSM2802428 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561521 + SAMN07729926 + GSM2802428 + + U87 scRNA-Seq U87_SC_h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561521 + SAMN07729926 + GSM2802428 + + + + + + + SRR6125142 + GSM2802428_r1 + + + + + + SRS2561521 + SAMN07729926 + GSM2802428 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237794 + + GSM2802427: U87 scRNA-Seq U87_SC_h12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561520 + GSM2802427 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802427 + + + + + + + GEO Accession + GSM2802427 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561520 + SAMN07729927 + GSM2802427 + + U87 scRNA-Seq U87_SC_h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561520 + SAMN07729927 + GSM2802427 + + + + + + + SRR6125141 + GSM2802427_r1 + + + + + + SRS2561520 + SAMN07729927 + GSM2802427 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237793 + + GSM2802426: U87 scRNA-Seq U87_SC_h11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561519 + GSM2802426 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802426 + + + + + + + GEO Accession + GSM2802426 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561519 + SAMN07729928 + GSM2802426 + + U87 scRNA-Seq U87_SC_h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561519 + SAMN07729928 + GSM2802426 + + + + + + + SRR6125140 + GSM2802426_r1 + + + + + + SRS2561519 + SAMN07729928 + GSM2802426 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237792 + + GSM2802425: U87 scRNA-Seq U87_SC_h10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561518 + GSM2802425 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802425 + + + + + + + GEO Accession + GSM2802425 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561518 + SAMN07729929 + GSM2802425 + + U87 scRNA-Seq U87_SC_h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561518 + SAMN07729929 + GSM2802425 + + + + + + + SRR6125139 + GSM2802425_r1 + + + + + + SRS2561518 + SAMN07729929 + GSM2802425 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237791 + + GSM2802424: U87 scRNA-Seq U87_SC_h1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561517 + GSM2802424 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802424 + + + + + + + GEO Accession + GSM2802424 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561517 + SAMN07729930 + GSM2802424 + + U87 scRNA-Seq U87_SC_h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561517 + SAMN07729930 + GSM2802424 + + + + + + + SRR6125138 + GSM2802424_r1 + + + + + + SRS2561517 + SAMN07729930 + GSM2802424 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237790 + + GSM2802423: U87 scRNA-Seq U87_SC_g9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561516 + GSM2802423 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802423 + + + + + + + GEO Accession + GSM2802423 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561516 + SAMN07729931 + GSM2802423 + + U87 scRNA-Seq U87_SC_g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561516 + SAMN07729931 + GSM2802423 + + + + + + + SRR6125137 + GSM2802423_r1 + + + + + + SRS2561516 + SAMN07729931 + GSM2802423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237789 + + GSM2802422: U87 scRNA-Seq U87_SC_g8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561515 + GSM2802422 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802422 + + + + + + + GEO Accession + GSM2802422 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561515 + SAMN07729932 + GSM2802422 + + U87 scRNA-Seq U87_SC_g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561515 + SAMN07729932 + GSM2802422 + + + + + + + SRR6125136 + GSM2802422_r1 + + + + + + SRS2561515 + SAMN07729932 + GSM2802422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237788 + + GSM2802421: U87 scRNA-Seq U87_SC_g7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561514 + GSM2802421 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802421 + + + + + + + GEO Accession + GSM2802421 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561514 + SAMN07729933 + GSM2802421 + + U87 scRNA-Seq U87_SC_g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561514 + SAMN07729933 + GSM2802421 + + + + + + + SRR6125135 + GSM2802421_r1 + + + + + + SRS2561514 + SAMN07729933 + GSM2802421 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237787 + + GSM2802420: U87 scRNA-Seq U87_SC_g6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561513 + GSM2802420 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802420 + + + + + + + GEO Accession + GSM2802420 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561513 + SAMN07729934 + GSM2802420 + + U87 scRNA-Seq U87_SC_g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561513 + SAMN07729934 + GSM2802420 + + + + + + + SRR6125134 + GSM2802420_r1 + + + + + + SRS2561513 + SAMN07729934 + GSM2802420 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237786 + + GSM2802419: U87 scRNA-Seq U87_SC_g5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561512 + GSM2802419 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802419 + + + + + + + GEO Accession + GSM2802419 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561512 + SAMN07729935 + GSM2802419 + + U87 scRNA-Seq U87_SC_g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561512 + SAMN07729935 + GSM2802419 + + + + + + + SRR6125133 + GSM2802419_r1 + + + + + + SRS2561512 + SAMN07729935 + GSM2802419 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237785 + + GSM2802418: U87 scRNA-Seq U87_SC_g4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561511 + GSM2802418 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802418 + + + + + + + GEO Accession + GSM2802418 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561511 + SAMN07730440 + GSM2802418 + + U87 scRNA-Seq U87_SC_g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561511 + SAMN07730440 + GSM2802418 + + + + + + + SRR6125132 + GSM2802418_r1 + + + + + + SRS2561511 + SAMN07730440 + GSM2802418 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237784 + + GSM2802417: U87 scRNA-Seq U87_SC_g3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561530 + GSM2802417 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802417 + + + + + + + GEO Accession + GSM2802417 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561530 + SAMN07730441 + GSM2802417 + + U87 scRNA-Seq U87_SC_g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561530 + SAMN07730441 + GSM2802417 + + + + + + + SRR6125131 + GSM2802417_r1 + + + + + + SRS2561530 + SAMN07730441 + GSM2802417 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237783 + + GSM2802416: U87 scRNA-Seq U87_SC_g2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561510 + GSM2802416 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802416 + + + + + + + GEO Accession + GSM2802416 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561510 + SAMN07730442 + GSM2802416 + + U87 scRNA-Seq U87_SC_g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561510 + SAMN07730442 + GSM2802416 + + + + + + + SRR6125130 + GSM2802416_r1 + + + + + + SRS2561510 + SAMN07730442 + GSM2802416 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237782 + + GSM2802415: U87 scRNA-Seq U87_SC_g12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561509 + GSM2802415 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802415 + + + + + + + GEO Accession + GSM2802415 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561509 + SAMN07730443 + GSM2802415 + + U87 scRNA-Seq U87_SC_g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561509 + SAMN07730443 + GSM2802415 + + + + + + + SRR6125129 + GSM2802415_r1 + + + + + + SRS2561509 + SAMN07730443 + GSM2802415 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237781 + + GSM2802414: U87 scRNA-Seq U87_SC_g11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561508 + GSM2802414 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802414 + + + + + + + GEO Accession + GSM2802414 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561508 + SAMN07730444 + GSM2802414 + + U87 scRNA-Seq U87_SC_g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561508 + SAMN07730444 + GSM2802414 + + + + + + + SRR6125128 + GSM2802414_r1 + + + + + + SRS2561508 + SAMN07730444 + GSM2802414 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237780 + + GSM2802413: U87 scRNA-Seq U87_SC_g10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561507 + GSM2802413 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802413 + + + + + + + GEO Accession + GSM2802413 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561507 + SAMN07730445 + GSM2802413 + + U87 scRNA-Seq U87_SC_g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561507 + SAMN07730445 + GSM2802413 + + + + + + + SRR6125127 + GSM2802413_r1 + + + + + + SRS2561507 + SAMN07730445 + GSM2802413 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237779 + + GSM2802412: U87 scRNA-Seq U87_SC_g1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561506 + GSM2802412 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802412 + + + + + + + GEO Accession + GSM2802412 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561506 + SAMN07730446 + GSM2802412 + + U87 scRNA-Seq U87_SC_g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561506 + SAMN07730446 + GSM2802412 + + + + + + + SRR6125126 + GSM2802412_r1 + + + + + + SRS2561506 + SAMN07730446 + GSM2802412 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237778 + + GSM2802411: U87 scRNA-Seq U87_SC_f9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561505 + GSM2802411 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802411 + + + + + + + GEO Accession + GSM2802411 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561505 + SAMN07730447 + GSM2802411 + + U87 scRNA-Seq U87_SC_f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561505 + SAMN07730447 + GSM2802411 + + + + + + + SRR6125125 + GSM2802411_r1 + + + + + + SRS2561505 + SAMN07730447 + GSM2802411 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237777 + + GSM2802410: U87 scRNA-Seq U87_SC_f8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561504 + GSM2802410 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802410 + + + + + + + GEO Accession + GSM2802410 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561504 + SAMN07730448 + GSM2802410 + + U87 scRNA-Seq U87_SC_f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561504 + SAMN07730448 + GSM2802410 + + + + + + + SRR6125124 + GSM2802410_r1 + + + + + + SRS2561504 + SAMN07730448 + GSM2802410 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237776 + + GSM2802409: U87 scRNA-Seq U87_SC_f7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561503 + GSM2802409 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802409 + + + + + + + GEO Accession + GSM2802409 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561503 + SAMN07730449 + GSM2802409 + + U87 scRNA-Seq U87_SC_f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561503 + SAMN07730449 + GSM2802409 + + + + + + + SRR6125123 + GSM2802409_r1 + + + + + + SRS2561503 + SAMN07730449 + GSM2802409 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237775 + + GSM2802408: U87 scRNA-Seq U87_SC_f6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561502 + GSM2802408 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802408 + + + + + + + GEO Accession + GSM2802408 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561502 + SAMN07730450 + GSM2802408 + + U87 scRNA-Seq U87_SC_f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561502 + SAMN07730450 + GSM2802408 + + + + + + + SRR6125122 + GSM2802408_r1 + + + + + + SRS2561502 + SAMN07730450 + GSM2802408 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237774 + + GSM2802407: U87 scRNA-Seq U87_SC_f5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561500 + GSM2802407 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802407 + + + + + + + GEO Accession + GSM2802407 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561500 + SAMN07730451 + GSM2802407 + + U87 scRNA-Seq U87_SC_f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561500 + SAMN07730451 + GSM2802407 + + + + + + + SRR6125121 + GSM2802407_r1 + + + + + + SRS2561500 + SAMN07730451 + GSM2802407 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237773 + + GSM2802406: U87 scRNA-Seq U87_SC_f4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561501 + GSM2802406 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802406 + + + + + + + GEO Accession + GSM2802406 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561501 + SAMN07730452 + GSM2802406 + + U87 scRNA-Seq U87_SC_f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561501 + SAMN07730452 + GSM2802406 + + + + + + + SRR6125120 + GSM2802406_r1 + + + + + + SRS2561501 + SAMN07730452 + GSM2802406 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237772 + + GSM2802405: U87 scRNA-Seq U87_SC_f3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561498 + GSM2802405 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802405 + + + + + + + GEO Accession + GSM2802405 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561498 + SAMN07730453 + GSM2802405 + + U87 scRNA-Seq U87_SC_f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561498 + SAMN07730453 + GSM2802405 + + + + + + + SRR6125119 + GSM2802405_r1 + + + + + + SRS2561498 + SAMN07730453 + GSM2802405 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237771 + + GSM2802404: U87 scRNA-Seq U87_SC_f2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561499 + GSM2802404 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802404 + + + + + + + GEO Accession + GSM2802404 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561499 + SAMN07730454 + GSM2802404 + + U87 scRNA-Seq U87_SC_f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561499 + SAMN07730454 + GSM2802404 + + + + + + + SRR6125118 + GSM2802404_r1 + + + + + + SRS2561499 + SAMN07730454 + GSM2802404 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237770 + + GSM2802403: U87 scRNA-Seq U87_SC_f12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561497 + GSM2802403 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802403 + + + + + + + GEO Accession + GSM2802403 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561497 + SAMN07730455 + GSM2802403 + + U87 scRNA-Seq U87_SC_f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561497 + SAMN07730455 + GSM2802403 + + + + + + + SRR6125117 + GSM2802403_r1 + + + + + + SRS2561497 + SAMN07730455 + GSM2802403 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237769 + + GSM2802402: U87 scRNA-Seq U87_SC_f11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561496 + GSM2802402 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802402 + + + + + + + GEO Accession + GSM2802402 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561496 + SAMN07730456 + GSM2802402 + + U87 scRNA-Seq U87_SC_f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561496 + SAMN07730456 + GSM2802402 + + + + + + + SRR6125116 + GSM2802402_r1 + + + + + + SRS2561496 + SAMN07730456 + GSM2802402 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237768 + + GSM2802401: U87 scRNA-Seq U87_SC_f10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561495 + GSM2802401 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802401 + + + + + + + GEO Accession + GSM2802401 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561495 + SAMN07730457 + GSM2802401 + + U87 scRNA-Seq U87_SC_f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561495 + SAMN07730457 + GSM2802401 + + + + + + + SRR6125115 + GSM2802401_r1 + + + + + + SRS2561495 + SAMN07730457 + GSM2802401 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237767 + + GSM2802400: U87 scRNA-Seq U87_SC_f1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561494 + GSM2802400 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802400 + + + + + + + GEO Accession + GSM2802400 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561494 + SAMN07730458 + GSM2802400 + + U87 scRNA-Seq U87_SC_f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561494 + SAMN07730458 + GSM2802400 + + + + + + + SRR6125114 + GSM2802400_r1 + + + + + + SRS2561494 + SAMN07730458 + GSM2802400 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237766 + + GSM2802399: U87 scRNA-Seq U87_SC_e9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561493 + GSM2802399 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802399 + + + + + + + GEO Accession + GSM2802399 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561493 + SAMN07730459 + GSM2802399 + + U87 scRNA-Seq U87_SC_e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561493 + SAMN07730459 + GSM2802399 + + + + + + + SRR6125113 + GSM2802399_r1 + + + + + + SRS2561493 + SAMN07730459 + GSM2802399 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237765 + + GSM2802398: U87 scRNA-Seq U87_SC_e8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561492 + GSM2802398 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802398 + + + + + + + GEO Accession + GSM2802398 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561492 + SAMN07730460 + GSM2802398 + + U87 scRNA-Seq U87_SC_e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561492 + SAMN07730460 + GSM2802398 + + + + + + + SRR6125112 + GSM2802398_r1 + + + + + + SRS2561492 + SAMN07730460 + GSM2802398 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237764 + + GSM2802397: U87 scRNA-Seq U87_SC_e7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561491 + GSM2802397 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802397 + + + + + + + GEO Accession + GSM2802397 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561491 + SAMN07730461 + GSM2802397 + + U87 scRNA-Seq U87_SC_e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561491 + SAMN07730461 + GSM2802397 + + + + + + + SRR6125111 + GSM2802397_r1 + + + + + + SRS2561491 + SAMN07730461 + GSM2802397 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237763 + + GSM2802396: U87 scRNA-Seq U87_SC_e6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561490 + GSM2802396 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802396 + + + + + + + GEO Accession + GSM2802396 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561490 + SAMN07730462 + GSM2802396 + + U87 scRNA-Seq U87_SC_e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561490 + SAMN07730462 + GSM2802396 + + + + + + + SRR6125110 + GSM2802396_r1 + + + + + + SRS2561490 + SAMN07730462 + GSM2802396 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237762 + + GSM2802395: U87 scRNA-Seq U87_SC_e5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561489 + GSM2802395 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802395 + + + + + + + GEO Accession + GSM2802395 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561489 + SAMN07730463 + GSM2802395 + + U87 scRNA-Seq U87_SC_e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561489 + SAMN07730463 + GSM2802395 + + + + + + + SRR6125109 + GSM2802395_r1 + + + + + + SRS2561489 + SAMN07730463 + GSM2802395 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237761 + + GSM2802394: U87 scRNA-Seq U87_SC_e4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561488 + GSM2802394 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802394 + + + + + + + GEO Accession + GSM2802394 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561488 + SAMN07730464 + GSM2802394 + + U87 scRNA-Seq U87_SC_e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561488 + SAMN07730464 + GSM2802394 + + + + + + + SRR6125108 + GSM2802394_r1 + + + + + + SRS2561488 + SAMN07730464 + GSM2802394 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237760 + + GSM2802393: U87 scRNA-Seq U87_SC_e3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561485 + GSM2802393 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802393 + + + + + + + GEO Accession + GSM2802393 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561485 + SAMN07730465 + GSM2802393 + + U87 scRNA-Seq U87_SC_e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561485 + SAMN07730465 + GSM2802393 + + + + + + + SRR6125107 + GSM2802393_r1 + + + + + + SRS2561485 + SAMN07730465 + GSM2802393 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237759 + + GSM2802392: U87 scRNA-Seq U87_SC_e2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561487 + GSM2802392 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802392 + + + + + + + GEO Accession + GSM2802392 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561487 + SAMN07730466 + GSM2802392 + + U87 scRNA-Seq U87_SC_e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561487 + SAMN07730466 + GSM2802392 + + + + + + + SRR6125106 + GSM2802392_r1 + + + + + + SRS2561487 + SAMN07730466 + GSM2802392 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237758 + + GSM2802391: U87 scRNA-Seq U87_SC_e12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561486 + GSM2802391 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802391 + + + + + + + GEO Accession + GSM2802391 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561486 + SAMN07730467 + GSM2802391 + + U87 scRNA-Seq U87_SC_e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561486 + SAMN07730467 + GSM2802391 + + + + + + + SRR6125105 + GSM2802391_r1 + + + + + + SRS2561486 + SAMN07730467 + GSM2802391 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237757 + + GSM2802390: U87 scRNA-Seq U87_SC_e11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561484 + GSM2802390 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802390 + + + + + + + GEO Accession + GSM2802390 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561484 + SAMN07730468 + GSM2802390 + + U87 scRNA-Seq U87_SC_e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561484 + SAMN07730468 + GSM2802390 + + + + + + + SRR6125104 + GSM2802390_r1 + + + + + + SRS2561484 + SAMN07730468 + GSM2802390 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237756 + + GSM2802389: U87 scRNA-Seq U87_SC_e10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561483 + GSM2802389 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802389 + + + + + + + GEO Accession + GSM2802389 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561483 + SAMN07730469 + GSM2802389 + + U87 scRNA-Seq U87_SC_e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561483 + SAMN07730469 + GSM2802389 + + + + + + + SRR6125103 + GSM2802389_r1 + + + + + + SRS2561483 + SAMN07730469 + GSM2802389 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237755 + + GSM2802388: U87 scRNA-Seq U87_SC_e1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561482 + GSM2802388 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802388 + + + + + + + GEO Accession + GSM2802388 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561482 + SAMN07729879 + GSM2802388 + + U87 scRNA-Seq U87_SC_e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561482 + SAMN07729879 + GSM2802388 + + + + + + + SRR6125102 + GSM2802388_r1 + + + + + + SRS2561482 + SAMN07729879 + GSM2802388 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237754 + + GSM2802387: U87 scRNA-Seq U87_SC_d9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561479 + GSM2802387 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802387 + + + + + + + GEO Accession + GSM2802387 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561479 + SAMN07729880 + GSM2802387 + + U87 scRNA-Seq U87_SC_d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561479 + SAMN07729880 + GSM2802387 + + + + + + + SRR6125101 + GSM2802387_r1 + + + + + + SRS2561479 + SAMN07729880 + GSM2802387 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237753 + + GSM2802386: U87 scRNA-Seq U87_SC_d8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561481 + GSM2802386 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802386 + + + + + + + GEO Accession + GSM2802386 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561481 + SAMN07729881 + GSM2802386 + + U87 scRNA-Seq U87_SC_d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561481 + SAMN07729881 + GSM2802386 + + + + + + + SRR6125100 + GSM2802386_r1 + + + + + + SRS2561481 + SAMN07729881 + GSM2802386 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237752 + + GSM2802385: U87 scRNA-Seq U87_SC_d7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561480 + GSM2802385 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802385 + + + + + + + GEO Accession + GSM2802385 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561480 + SAMN07729882 + GSM2802385 + + U87 scRNA-Seq U87_SC_d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561480 + SAMN07729882 + GSM2802385 + + + + + + + SRR6125099 + GSM2802385_r1 + + + + + + SRS2561480 + SAMN07729882 + GSM2802385 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237751 + + GSM2802384: U87 scRNA-Seq U87_SC_d6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561478 + GSM2802384 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802384 + + + + + + + GEO Accession + GSM2802384 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561478 + SAMN07729883 + GSM2802384 + + U87 scRNA-Seq U87_SC_d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561478 + SAMN07729883 + GSM2802384 + + + + + + + SRR6125098 + GSM2802384_r1 + + + + + + SRS2561478 + SAMN07729883 + GSM2802384 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237750 + + GSM2802383: U87 scRNA-Seq U87_SC_d5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561477 + GSM2802383 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802383 + + + + + + + GEO Accession + GSM2802383 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561477 + SAMN07729884 + GSM2802383 + + U87 scRNA-Seq U87_SC_d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561477 + SAMN07729884 + GSM2802383 + + + + + + + SRR6125097 + GSM2802383_r1 + + + + + + SRS2561477 + SAMN07729884 + GSM2802383 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237749 + + GSM2802382: U87 scRNA-Seq U87_SC_d4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561476 + GSM2802382 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802382 + + + + + + + GEO Accession + GSM2802382 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561476 + SAMN07729885 + GSM2802382 + + U87 scRNA-Seq U87_SC_d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561476 + SAMN07729885 + GSM2802382 + + + + + + + SRR6125096 + GSM2802382_r1 + + + + + + SRS2561476 + SAMN07729885 + GSM2802382 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237748 + + GSM2802381: U87 scRNA-Seq U87_SC_d3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561475 + GSM2802381 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802381 + + + + + + + GEO Accession + GSM2802381 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561475 + SAMN07729886 + GSM2802381 + + U87 scRNA-Seq U87_SC_d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561475 + SAMN07729886 + GSM2802381 + + + + + + + SRR6125095 + GSM2802381_r1 + + + + + + SRS2561475 + SAMN07729886 + GSM2802381 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237747 + + GSM2802380: U87 scRNA-Seq U87_SC_d2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561474 + GSM2802380 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802380 + + + + + + + GEO Accession + GSM2802380 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561474 + SAMN07729887 + GSM2802380 + + U87 scRNA-Seq U87_SC_d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561474 + SAMN07729887 + GSM2802380 + + + + + + + SRR6125094 + GSM2802380_r1 + + + + + + SRS2561474 + SAMN07729887 + GSM2802380 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237746 + + GSM2802379: U87 scRNA-Seq U87_SC_d12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561473 + GSM2802379 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802379 + + + + + + + GEO Accession + GSM2802379 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561473 + SAMN07729888 + GSM2802379 + + U87 scRNA-Seq U87_SC_d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561473 + SAMN07729888 + GSM2802379 + + + + + + + SRR6125093 + GSM2802379_r1 + + + + + + SRS2561473 + SAMN07729888 + GSM2802379 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237745 + + GSM2802378: U87 scRNA-Seq U87_SC_d11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561472 + GSM2802378 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802378 + + + + + + + GEO Accession + GSM2802378 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561472 + SAMN07729889 + GSM2802378 + + U87 scRNA-Seq U87_SC_d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561472 + SAMN07729889 + GSM2802378 + + + + + + + SRR6125092 + GSM2802378_r1 + + + + + + SRS2561472 + SAMN07729889 + GSM2802378 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237744 + + GSM2802377: U87 scRNA-Seq U87_SC_d10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561471 + GSM2802377 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802377 + + + + + + + GEO Accession + GSM2802377 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561471 + SAMN07730500 + GSM2802377 + + U87 scRNA-Seq U87_SC_d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561471 + SAMN07730500 + GSM2802377 + + + + + + + SRR6125091 + GSM2802377_r1 + + + + + + SRS2561471 + SAMN07730500 + GSM2802377 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237743 + + GSM2802376: U87 scRNA-Seq U87_SC_d1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561470 + GSM2802376 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802376 + + + + + + + GEO Accession + GSM2802376 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561470 + SAMN07730501 + GSM2802376 + + U87 scRNA-Seq U87_SC_d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561470 + SAMN07730501 + GSM2802376 + + + + + + + SRR6125090 + GSM2802376_r1 + + + + + + SRS2561470 + SAMN07730501 + GSM2802376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237742 + + GSM2802375: U87 scRNA-Seq U87_SC_c9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561469 + GSM2802375 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802375 + + + + + + + GEO Accession + GSM2802375 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561469 + SAMN07730502 + GSM2802375 + + U87 scRNA-Seq U87_SC_c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561469 + SAMN07730502 + GSM2802375 + + + + + + + SRR6125089 + GSM2802375_r1 + + + + + + SRS2561469 + SAMN07730502 + GSM2802375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237741 + + GSM2802374: U87 scRNA-Seq U87_SC_c8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561468 + GSM2802374 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802374 + + + + + + + GEO Accession + GSM2802374 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561468 + SAMN07730503 + GSM2802374 + + U87 scRNA-Seq U87_SC_c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561468 + SAMN07730503 + GSM2802374 + + + + + + + SRR6125088 + GSM2802374_r1 + + + + + + SRS2561468 + SAMN07730503 + GSM2802374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237740 + + GSM2802373: U87 scRNA-Seq U87_SC_c7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561467 + GSM2802373 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802373 + + + + + + + GEO Accession + GSM2802373 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561467 + SAMN07730504 + GSM2802373 + + U87 scRNA-Seq U87_SC_c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561467 + SAMN07730504 + GSM2802373 + + + + + + + SRR6125087 + GSM2802373_r1 + + + + + + SRS2561467 + SAMN07730504 + GSM2802373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237739 + + GSM2802372: U87 scRNA-Seq U87_SC_c6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561466 + GSM2802372 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802372 + + + + + + + GEO Accession + GSM2802372 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561466 + SAMN07730505 + GSM2802372 + + U87 scRNA-Seq U87_SC_c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561466 + SAMN07730505 + GSM2802372 + + + + + + + SRR6125086 + GSM2802372_r1 + + + + + + SRS2561466 + SAMN07730505 + GSM2802372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237738 + + GSM2802371: U87 scRNA-Seq U87_SC_c5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561465 + GSM2802371 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802371 + + + + + + + GEO Accession + GSM2802371 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561465 + SAMN07730506 + GSM2802371 + + U87 scRNA-Seq U87_SC_c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561465 + SAMN07730506 + GSM2802371 + + + + + + + SRR6125085 + GSM2802371_r1 + + + + + + SRS2561465 + SAMN07730506 + GSM2802371 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237737 + + GSM2802370: U87 scRNA-Seq U87_SC_c4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561464 + GSM2802370 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802370 + + + + + + + GEO Accession + GSM2802370 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561464 + SAMN07730507 + GSM2802370 + + U87 scRNA-Seq U87_SC_c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561464 + SAMN07730507 + GSM2802370 + + + + + + + SRR6125084 + GSM2802370_r1 + + + + + + SRS2561464 + SAMN07730507 + GSM2802370 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237736 + + GSM2802369: U87 scRNA-Seq U87_SC_c3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561463 + GSM2802369 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802369 + + + + + + + GEO Accession + GSM2802369 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561463 + SAMN07730508 + GSM2802369 + + U87 scRNA-Seq U87_SC_c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561463 + SAMN07730508 + GSM2802369 + + + + + + + SRR6125083 + GSM2802369_r1 + + + + + + SRS2561463 + SAMN07730508 + GSM2802369 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237735 + + GSM2802368: U87 scRNA-Seq U87_SC_c2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561462 + GSM2802368 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802368 + + + + + + + GEO Accession + GSM2802368 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561462 + SAMN07730509 + GSM2802368 + + U87 scRNA-Seq U87_SC_c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561462 + SAMN07730509 + GSM2802368 + + + + + + + SRR6125082 + GSM2802368_r1 + + + + + + SRS2561462 + SAMN07730509 + GSM2802368 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237734 + + GSM2802367: U87 scRNA-Seq U87_SC_c12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561461 + GSM2802367 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802367 + + + + + + + GEO Accession + GSM2802367 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561461 + SAMN07730510 + GSM2802367 + + U87 scRNA-Seq U87_SC_c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561461 + SAMN07730510 + GSM2802367 + + + + + + + SRR6125081 + GSM2802367_r1 + + + + + + SRS2561461 + SAMN07730510 + GSM2802367 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237733 + + GSM2802366: U87 scRNA-Seq U87_SC_c11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561460 + GSM2802366 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802366 + + + + + + + GEO Accession + GSM2802366 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561460 + SAMN07730511 + GSM2802366 + + U87 scRNA-Seq U87_SC_c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561460 + SAMN07730511 + GSM2802366 + + + + + + + SRR6125080 + GSM2802366_r1 + + + + + + SRS2561460 + SAMN07730511 + GSM2802366 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237732 + + GSM2802365: U87 scRNA-Seq U87_SC_c10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561459 + GSM2802365 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802365 + + + + + + + GEO Accession + GSM2802365 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561459 + SAMN07730512 + GSM2802365 + + U87 scRNA-Seq U87_SC_c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561459 + SAMN07730512 + GSM2802365 + + + + + + + SRR6125079 + GSM2802365_r1 + + + + + + SRS2561459 + SAMN07730512 + GSM2802365 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237731 + + GSM2802364: U87 scRNA-Seq U87_SC_c1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561458 + GSM2802364 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802364 + + + + + + + GEO Accession + GSM2802364 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561458 + SAMN07730513 + GSM2802364 + + U87 scRNA-Seq U87_SC_c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561458 + SAMN07730513 + GSM2802364 + + + + + + + SRR6125078 + GSM2802364_r1 + + + + + + SRS2561458 + SAMN07730513 + GSM2802364 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237730 + + GSM2802363: U87 scRNA-Seq U87_SC_b9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561457 + GSM2802363 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802363 + + + + + + + GEO Accession + GSM2802363 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561457 + SAMN07730514 + GSM2802363 + + U87 scRNA-Seq U87_SC_b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561457 + SAMN07730514 + GSM2802363 + + + + + + + SRR6125077 + GSM2802363_r1 + + + + + + SRS2561457 + SAMN07730514 + GSM2802363 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237729 + + GSM2802362: U87 scRNA-Seq U87_SC_b8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561456 + GSM2802362 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802362 + + + + + + + GEO Accession + GSM2802362 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561456 + SAMN07730515 + GSM2802362 + + U87 scRNA-Seq U87_SC_b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561456 + SAMN07730515 + GSM2802362 + + + + + + + SRR6125076 + GSM2802362_r1 + + + + + + SRS2561456 + SAMN07730515 + GSM2802362 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237728 + + GSM2802361: U87 scRNA-Seq U87_SC_b7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561455 + GSM2802361 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802361 + + + + + + + GEO Accession + GSM2802361 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561455 + SAMN07730516 + GSM2802361 + + U87 scRNA-Seq U87_SC_b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561455 + SAMN07730516 + GSM2802361 + + + + + + + SRR6125075 + GSM2802361_r1 + + + + + + SRS2561455 + SAMN07730516 + GSM2802361 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237727 + + GSM2802360: U87 scRNA-Seq U87_SC_b6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561453 + GSM2802360 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802360 + + + + + + + GEO Accession + GSM2802360 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561453 + SAMN07730517 + GSM2802360 + + U87 scRNA-Seq U87_SC_b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561453 + SAMN07730517 + GSM2802360 + + + + + + + SRR6125074 + GSM2802360_r1 + + + + + + SRS2561453 + SAMN07730517 + GSM2802360 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237726 + + GSM2802359: U87 scRNA-Seq U87_SC_b5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561454 + GSM2802359 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802359 + + + + + + + GEO Accession + GSM2802359 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561454 + SAMN07730518 + GSM2802359 + + U87 scRNA-Seq U87_SC_b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561454 + SAMN07730518 + GSM2802359 + + + + + + + SRR6125073 + GSM2802359_r1 + + + + + + SRS2561454 + SAMN07730518 + GSM2802359 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237725 + + GSM2802358: U87 scRNA-Seq U87_SC_b4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561452 + GSM2802358 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802358 + + + + + + + GEO Accession + GSM2802358 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561452 + SAMN07730519 + GSM2802358 + + U87 scRNA-Seq U87_SC_b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561452 + SAMN07730519 + GSM2802358 + + + + + + + SRR6125072 + GSM2802358_r1 + + + + + + SRS2561452 + SAMN07730519 + GSM2802358 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237724 + + GSM2802357: U87 scRNA-Seq U87_SC_b3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561451 + GSM2802357 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802357 + + + + + + + GEO Accession + GSM2802357 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561451 + SAMN07730520 + GSM2802357 + + U87 scRNA-Seq U87_SC_b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561451 + SAMN07730520 + GSM2802357 + + + + + + + SRR6125071 + GSM2802357_r1 + + + + + + SRS2561451 + SAMN07730520 + GSM2802357 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237723 + + GSM2802356: U87 scRNA-Seq U87_SC_b2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561450 + GSM2802356 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802356 + + + + + + + GEO Accession + GSM2802356 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561450 + SAMN07730521 + GSM2802356 + + U87 scRNA-Seq U87_SC_b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561450 + SAMN07730521 + GSM2802356 + + + + + + + SRR6125070 + GSM2802356_r1 + + + + + + SRS2561450 + SAMN07730521 + GSM2802356 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237722 + + GSM2802355: U87 scRNA-Seq U87_SC_b12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561449 + GSM2802355 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802355 + + + + + + + GEO Accession + GSM2802355 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561449 + SAMN07730522 + GSM2802355 + + U87 scRNA-Seq U87_SC_b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561449 + SAMN07730522 + GSM2802355 + + + + + + + SRR6125069 + GSM2802355_r1 + + + + + + SRS2561449 + SAMN07730522 + GSM2802355 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237721 + + GSM2802354: U87 scRNA-Seq U87_SC_b11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561447 + GSM2802354 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802354 + + + + + + + GEO Accession + GSM2802354 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561447 + SAMN07730523 + GSM2802354 + + U87 scRNA-Seq U87_SC_b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561447 + SAMN07730523 + GSM2802354 + + + + + + + SRR6125068 + GSM2802354_r1 + + + + + + SRS2561447 + SAMN07730523 + GSM2802354 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237720 + + GSM2802353: U87 scRNA-Seq U87_SC_b10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561448 + GSM2802353 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802353 + + + + + + + GEO Accession + GSM2802353 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561448 + SAMN07730524 + GSM2802353 + + U87 scRNA-Seq U87_SC_b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561448 + SAMN07730524 + GSM2802353 + + + + + + + SRR6125067 + GSM2802353_r1 + + + + + + SRS2561448 + SAMN07730524 + GSM2802353 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237719 + + GSM2802352: U87 scRNA-Seq U87_SC_b1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561446 + GSM2802352 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802352 + + + + + + + GEO Accession + GSM2802352 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561446 + SAMN07730525 + GSM2802352 + + U87 scRNA-Seq U87_SC_b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561446 + SAMN07730525 + GSM2802352 + + + + + + + SRR6125066 + GSM2802352_r1 + + + + + + SRS2561446 + SAMN07730525 + GSM2802352 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237718 + + GSM2802351: U87 scRNA-Seq U87_SC_a9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561445 + GSM2802351 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802351 + + + + + + + GEO Accession + GSM2802351 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561445 + SAMN07730526 + GSM2802351 + + U87 scRNA-Seq U87_SC_a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561445 + SAMN07730526 + GSM2802351 + + + + + + + SRR6125065 + GSM2802351_r1 + + + + + + SRS2561445 + SAMN07730526 + GSM2802351 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237717 + + GSM2802350: U87 scRNA-Seq U87_SC_a8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561444 + GSM2802350 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802350 + + + + + + + GEO Accession + GSM2802350 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561444 + SAMN07730527 + GSM2802350 + + U87 scRNA-Seq U87_SC_a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561444 + SAMN07730527 + GSM2802350 + + + + + + + SRR6125064 + GSM2802350_r1 + + + + + + SRS2561444 + SAMN07730527 + GSM2802350 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237716 + + GSM2802349: U87 scRNA-Seq U87_SC_a7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561443 + GSM2802349 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802349 + + + + + + + GEO Accession + GSM2802349 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561443 + SAMN07730528 + GSM2802349 + + U87 scRNA-Seq U87_SC_a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561443 + SAMN07730528 + GSM2802349 + + + + + + + SRR6125063 + GSM2802349_r1 + + + + + + SRS2561443 + SAMN07730528 + GSM2802349 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237715 + + GSM2802348: U87 scRNA-Seq U87_SC_a6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561442 + GSM2802348 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802348 + + + + + + + GEO Accession + GSM2802348 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561442 + SAMN07730529 + GSM2802348 + + U87 scRNA-Seq U87_SC_a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561442 + SAMN07730529 + GSM2802348 + + + + + + + SRR6125062 + GSM2802348_r1 + + + + + + SRS2561442 + SAMN07730529 + GSM2802348 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237714 + + GSM2802347: U87 scRNA-Seq U87_SC_a5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561441 + GSM2802347 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802347 + + + + + + + GEO Accession + GSM2802347 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561441 + SAMN07730263 + GSM2802347 + + U87 scRNA-Seq U87_SC_a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561441 + SAMN07730263 + GSM2802347 + + + + + + + SRR6125061 + GSM2802347_r1 + + + + + + SRS2561441 + SAMN07730263 + GSM2802347 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237713 + + GSM2802346: U87 scRNA-Seq U87_SC_a4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561440 + GSM2802346 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802346 + + + + + + + GEO Accession + GSM2802346 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561440 + SAMN07730264 + GSM2802346 + + U87 scRNA-Seq U87_SC_a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561440 + SAMN07730264 + GSM2802346 + + + + + + + SRR6125060 + GSM2802346_r1 + + + + + + SRS2561440 + SAMN07730264 + GSM2802346 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237712 + + GSM2802345: U87 scRNA-Seq U87_SC_a3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561439 + GSM2802345 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802345 + + + + + + + GEO Accession + GSM2802345 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561439 + SAMN07730265 + GSM2802345 + + U87 scRNA-Seq U87_SC_a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561439 + SAMN07730265 + GSM2802345 + + + + + + + SRR6125059 + GSM2802345_r1 + + + + + + SRS2561439 + SAMN07730265 + GSM2802345 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237711 + + GSM2802344: U87 scRNA-Seq U87_SC_a2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561438 + GSM2802344 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802344 + + + + + + + GEO Accession + GSM2802344 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561438 + SAMN07730266 + GSM2802344 + + U87 scRNA-Seq U87_SC_a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561438 + SAMN07730266 + GSM2802344 + + + + + + + SRR6125058 + GSM2802344_r1 + + + + + + SRS2561438 + SAMN07730266 + GSM2802344 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237710 + + GSM2802343: U87 scRNA-Seq U87_SC_a12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561437 + GSM2802343 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802343 + + + + + + + GEO Accession + GSM2802343 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561437 + SAMN07730267 + GSM2802343 + + U87 scRNA-Seq U87_SC_a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561437 + SAMN07730267 + GSM2802343 + + + + + + + SRR6125057 + GSM2802343_r1 + + + + + + SRS2561437 + SAMN07730267 + GSM2802343 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237709 + + GSM2802342: U87 scRNA-Seq U87_SC_a11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561436 + GSM2802342 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802342 + + + + + + + GEO Accession + GSM2802342 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561436 + SAMN07730268 + GSM2802342 + + U87 scRNA-Seq U87_SC_a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561436 + SAMN07730268 + GSM2802342 + + + + + + + SRR6125056 + GSM2802342_r1 + + + + + + SRS2561436 + SAMN07730268 + GSM2802342 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237708 + + GSM2802341: U87 scRNA-Seq U87_SC_a10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561435 + GSM2802341 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802341 + + + + + + + GEO Accession + GSM2802341 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561435 + SAMN07730269 + GSM2802341 + + U87 scRNA-Seq U87_SC_a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561435 + SAMN07730269 + GSM2802341 + + + + + + + SRR6125055 + GSM2802341_r1 + + + + + + SRS2561435 + SAMN07730269 + GSM2802341 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237707 + + GSM2802340: U87 scRNA-Seq U87_SC_a1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561434 + GSM2802340 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802340 + + + + + + + GEO Accession + GSM2802340 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561434 + SAMN07730270 + GSM2802340 + + U87 scRNA-Seq U87_SC_a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured U87 cells + + + cell line + U87 + + + + + + + SRS2561434 + SAMN07730270 + GSM2802340 + + + + + + + SRR6125054 + GSM2802340_r1 + + + + + + SRS2561434 + SAMN07730270 + GSM2802340 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237706 + + GSM2802339: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561433 + GSM2802339 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802339 + + + + + + + GEO Accession + GSM2802339 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561433 + SAMN07730271 + GSM2802339 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561433 + SAMN07730271 + GSM2802339 + + + + + + + SRR6125053 + GSM2802339_r1 + + + + + + SRS2561433 + SAMN07730271 + GSM2802339 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237705 + + GSM2802338: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561432 + GSM2802338 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802338 + + + + + + + GEO Accession + GSM2802338 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561432 + SAMN07730272 + GSM2802338 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561432 + SAMN07730272 + GSM2802338 + + + + + + + SRR6125052 + GSM2802338_r1 + + + + + + SRS2561432 + SAMN07730272 + GSM2802338 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237704 + + GSM2802337: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561431 + GSM2802337 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802337 + + + + + + + GEO Accession + GSM2802337 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561431 + SAMN07730273 + GSM2802337 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561431 + SAMN07730273 + GSM2802337 + + + + + + + SRR6125051 + GSM2802337_r1 + + + + + + SRS2561431 + SAMN07730273 + GSM2802337 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237703 + + GSM2802336: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561430 + GSM2802336 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802336 + + + + + + + GEO Accession + GSM2802336 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561430 + SAMN07730274 + GSM2802336 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561430 + SAMN07730274 + GSM2802336 + + + + + + + SRR6125050 + GSM2802336_r1 + + + + + + SRS2561430 + SAMN07730274 + GSM2802336 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237702 + + GSM2802335: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561429 + GSM2802335 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802335 + + + + + + + GEO Accession + GSM2802335 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561429 + SAMN07730275 + GSM2802335 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561429 + SAMN07730275 + GSM2802335 + + + + + + + SRR6125049 + GSM2802335_r1 + + + + + + SRS2561429 + SAMN07730275 + GSM2802335 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237701 + + GSM2802334: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561428 + GSM2802334 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802334 + + + + + + + GEO Accession + GSM2802334 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561428 + SAMN07730276 + GSM2802334 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561428 + SAMN07730276 + GSM2802334 + + + + + + + SRR6125048 + GSM2802334_r1 + + + + + + SRS2561428 + SAMN07730276 + GSM2802334 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237700 + + GSM2802333: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561427 + GSM2802333 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802333 + + + + + + + GEO Accession + GSM2802333 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561427 + SAMN07730277 + GSM2802333 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561427 + SAMN07730277 + GSM2802333 + + + + + + + SRR6125047 + GSM2802333_r1 + + + + + + SRS2561427 + SAMN07730277 + GSM2802333 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237699 + + GSM2802332: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561426 + GSM2802332 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802332 + + + + + + + GEO Accession + GSM2802332 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561426 + SAMN07730278 + GSM2802332 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561426 + SAMN07730278 + GSM2802332 + + + + + + + SRR6125046 + GSM2802332_r1 + + + + + + SRS2561426 + SAMN07730278 + GSM2802332 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237698 + + GSM2802331: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561425 + GSM2802331 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802331 + + + + + + + GEO Accession + GSM2802331 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561425 + SAMN07730279 + GSM2802331 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561425 + SAMN07730279 + GSM2802331 + + + + + + + SRR6125045 + GSM2802331_r1 + + + + + + SRS2561425 + SAMN07730279 + GSM2802331 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237697 + + GSM2802330: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561424 + GSM2802330 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802330 + + + + + + + GEO Accession + GSM2802330 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561424 + SAMN07730280 + GSM2802330 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561424 + SAMN07730280 + GSM2802330 + + + + + + + SRR6125044 + GSM2802330_r1 + + + + + + SRS2561424 + SAMN07730280 + GSM2802330 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237696 + + GSM2802329: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561423 + GSM2802329 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802329 + + + + + + + GEO Accession + GSM2802329 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561423 + SAMN07730281 + GSM2802329 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561423 + SAMN07730281 + GSM2802329 + + + + + + + SRR6125043 + GSM2802329_r1 + + + + + + SRS2561423 + SAMN07730281 + GSM2802329 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237695 + + GSM2802328: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561422 + GSM2802328 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802328 + + + + + + + GEO Accession + GSM2802328 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561422 + SAMN07730282 + GSM2802328 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561422 + SAMN07730282 + GSM2802328 + + + + + + + SRR6125042 + GSM2802328_r1 + + + + + + SRS2561422 + SAMN07730282 + GSM2802328 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237694 + + GSM2802327: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561421 + GSM2802327 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802327 + + + + + + + GEO Accession + GSM2802327 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561421 + SAMN07730283 + GSM2802327 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561421 + SAMN07730283 + GSM2802327 + + + + + + + SRR6125041 + GSM2802327_r1 + + + + + + SRS2561421 + SAMN07730283 + GSM2802327 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237693 + + GSM2802326: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561420 + GSM2802326 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802326 + + + + + + + GEO Accession + GSM2802326 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561420 + SAMN07730284 + GSM2802326 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561420 + SAMN07730284 + GSM2802326 + + + + + + + SRR6125040 + GSM2802326_r1 + + + + + + SRS2561420 + SAMN07730284 + GSM2802326 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237692 + + GSM2802325: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561419 + GSM2802325 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802325 + + + + + + + GEO Accession + GSM2802325 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561419 + SAMN07730285 + GSM2802325 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561419 + SAMN07730285 + GSM2802325 + + + + + + + SRR6125039 + GSM2802325_r1 + + + + + + SRS2561419 + SAMN07730285 + GSM2802325 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237691 + + GSM2802324: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561418 + GSM2802324 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802324 + + + + + + + GEO Accession + GSM2802324 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561418 + SAMN07730286 + GSM2802324 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561418 + SAMN07730286 + GSM2802324 + + + + + + + SRR6125038 + GSM2802324_r1 + + + + + + SRS2561418 + SAMN07730286 + GSM2802324 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237690 + + GSM2802323: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561417 + GSM2802323 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802323 + + + + + + + GEO Accession + GSM2802323 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561417 + SAMN07730287 + GSM2802323 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561417 + SAMN07730287 + GSM2802323 + + + + + + + SRR6125037 + GSM2802323_r1 + + + + + + SRS2561417 + SAMN07730287 + GSM2802323 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237689 + + GSM2802322: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561416 + GSM2802322 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802322 + + + + + + + GEO Accession + GSM2802322 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561416 + SAMN07730288 + GSM2802322 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561416 + SAMN07730288 + GSM2802322 + + + + + + + SRR6125036 + GSM2802322_r1 + + + + + + SRS2561416 + SAMN07730288 + GSM2802322 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237688 + + GSM2802321: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561415 + GSM2802321 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802321 + + + + + + + GEO Accession + GSM2802321 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561415 + SAMN07730289 + GSM2802321 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561415 + SAMN07730289 + GSM2802321 + + + + + + + SRR6125035 + GSM2802321_r1 + + + + + + SRS2561415 + SAMN07730289 + GSM2802321 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237687 + + GSM2802320: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561414 + GSM2802320 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802320 + + + + + + + GEO Accession + GSM2802320 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561414 + SAMN07730290 + GSM2802320 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561414 + SAMN07730290 + GSM2802320 + + + + + + + SRR6125034 + GSM2802320_r1 + + + + + + SRS2561414 + SAMN07730290 + GSM2802320 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237686 + + GSM2802319: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561413 + GSM2802319 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802319 + + + + + + + GEO Accession + GSM2802319 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561413 + SAMN07730291 + GSM2802319 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561413 + SAMN07730291 + GSM2802319 + + + + + + + SRR6125033 + GSM2802319_r1 + + + + + + SRS2561413 + SAMN07730291 + GSM2802319 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237685 + + GSM2802318: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561412 + GSM2802318 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802318 + + + + + + + GEO Accession + GSM2802318 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561412 + SAMN07730292 + GSM2802318 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561412 + SAMN07730292 + GSM2802318 + + + + + + + SRR6125032 + GSM2802318_r1 + + + + + + SRS2561412 + SAMN07730292 + GSM2802318 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237684 + + GSM2802317: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561411 + GSM2802317 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802317 + + + + + + + GEO Accession + GSM2802317 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561411 + SAMN07730410 + GSM2802317 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561411 + SAMN07730410 + GSM2802317 + + + + + + + SRR6125031 + GSM2802317_r1 + + + + + + SRS2561411 + SAMN07730410 + GSM2802317 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237683 + + GSM2802316: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561410 + GSM2802316 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802316 + + + + + + + GEO Accession + GSM2802316 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561410 + SAMN07730411 + GSM2802316 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561410 + SAMN07730411 + GSM2802316 + + + + + + + SRR6125030 + GSM2802316_r1 + + + + + + SRS2561410 + SAMN07730411 + GSM2802316 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237682 + + GSM2802315: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561409 + GSM2802315 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802315 + + + + + + + GEO Accession + GSM2802315 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561409 + SAMN07730412 + GSM2802315 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561409 + SAMN07730412 + GSM2802315 + + + + + + + SRR6125029 + GSM2802315_r1 + + + + + + SRS2561409 + SAMN07730412 + GSM2802315 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237681 + + GSM2802314: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561408 + GSM2802314 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802314 + + + + + + + GEO Accession + GSM2802314 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561408 + SAMN07730413 + GSM2802314 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561408 + SAMN07730413 + GSM2802314 + + + + + + + SRR6125028 + GSM2802314_r1 + + + + + + SRS2561408 + SAMN07730413 + GSM2802314 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237680 + + GSM2802313: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561407 + GSM2802313 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802313 + + + + + + + GEO Accession + GSM2802313 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561407 + SAMN07730414 + GSM2802313 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561407 + SAMN07730414 + GSM2802313 + + + + + + + SRR6125027 + GSM2802313_r1 + + + + + + SRS2561407 + SAMN07730414 + GSM2802313 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237679 + + GSM2802312: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561406 + GSM2802312 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802312 + + + + + + + GEO Accession + GSM2802312 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561406 + SAMN07730415 + GSM2802312 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561406 + SAMN07730415 + GSM2802312 + + + + + + + SRR6125026 + GSM2802312_r1 + + + + + + SRS2561406 + SAMN07730415 + GSM2802312 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237678 + + GSM2802311: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561405 + GSM2802311 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802311 + + + + + + + GEO Accession + GSM2802311 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561405 + SAMN07730416 + GSM2802311 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561405 + SAMN07730416 + GSM2802311 + + + + + + + SRR6125025 + GSM2802311_r1 + + + + + + SRS2561405 + SAMN07730416 + GSM2802311 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237677 + + GSM2802310: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561404 + GSM2802310 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802310 + + + + + + + GEO Accession + GSM2802310 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561404 + SAMN07730417 + GSM2802310 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561404 + SAMN07730417 + GSM2802310 + + + + + + + SRR6125024 + GSM2802310_r1 + + + + + + SRS2561404 + SAMN07730417 + GSM2802310 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237676 + + GSM2802309: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561403 + GSM2802309 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802309 + + + + + + + GEO Accession + GSM2802309 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561403 + SAMN07730418 + GSM2802309 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561403 + SAMN07730418 + GSM2802309 + + + + + + + SRR6125023 + GSM2802309_r1 + + + + + + SRS2561403 + SAMN07730418 + GSM2802309 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237675 + + GSM2802308: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561402 + GSM2802308 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802308 + + + + + + + GEO Accession + GSM2802308 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561402 + SAMN07730419 + GSM2802308 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561402 + SAMN07730419 + GSM2802308 + + + + + + + SRR6125022 + GSM2802308_r1 + + + + + + SRS2561402 + SAMN07730419 + GSM2802308 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237674 + + GSM2802307: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561401 + GSM2802307 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802307 + + + + + + + GEO Accession + GSM2802307 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561401 + SAMN07730420 + GSM2802307 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561401 + SAMN07730420 + GSM2802307 + + + + + + + SRR6125021 + GSM2802307_r1 + + + + + + SRS2561401 + SAMN07730420 + GSM2802307 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237673 + + GSM2802306: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561400 + GSM2802306 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802306 + + + + + + + GEO Accession + GSM2802306 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561400 + SAMN07730421 + GSM2802306 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561400 + SAMN07730421 + GSM2802306 + + + + + + + SRR6125020 + GSM2802306_r1 + + + + + + SRS2561400 + SAMN07730421 + GSM2802306 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237672 + + GSM2802305: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561399 + GSM2802305 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802305 + + + + + + + GEO Accession + GSM2802305 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561399 + SAMN07730422 + GSM2802305 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561399 + SAMN07730422 + GSM2802305 + + + + + + + SRR6125019 + GSM2802305_r1 + + + + + + SRS2561399 + SAMN07730422 + GSM2802305 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237671 + + GSM2802304: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561398 + GSM2802304 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802304 + + + + + + + GEO Accession + GSM2802304 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561398 + SAMN07730423 + GSM2802304 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561398 + SAMN07730423 + GSM2802304 + + + + + + + SRR6125018 + GSM2802304_r1 + + + + + + SRS2561398 + SAMN07730423 + GSM2802304 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237670 + + GSM2802303: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561397 + GSM2802303 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802303 + + + + + + + GEO Accession + GSM2802303 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561397 + SAMN07730424 + GSM2802303 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561397 + SAMN07730424 + GSM2802303 + + + + + + + SRR6125017 + GSM2802303_r1 + + + + + + SRS2561397 + SAMN07730424 + GSM2802303 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237669 + + GSM2802302: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561395 + GSM2802302 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802302 + + + + + + + GEO Accession + GSM2802302 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561395 + SAMN07730431 + GSM2802302 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561395 + SAMN07730431 + GSM2802302 + + + + + + + SRR6125016 + GSM2802302_r1 + + + + + + SRS2561395 + SAMN07730431 + GSM2802302 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237668 + + GSM2802301: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561396 + GSM2802301 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802301 + + + + + + + GEO Accession + GSM2802301 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561396 + SAMN07730425 + GSM2802301 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561396 + SAMN07730425 + GSM2802301 + + + + + + + SRR6125015 + GSM2802301_r1 + + + + + + SRS2561396 + SAMN07730425 + GSM2802301 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237667 + + GSM2802300: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561393 + GSM2802300 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802300 + + + + + + + GEO Accession + GSM2802300 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561393 + SAMN07730426 + GSM2802300 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561393 + SAMN07730426 + GSM2802300 + + + + + + + SRR6125014 + GSM2802300_r1 + + + + + + SRS2561393 + SAMN07730426 + GSM2802300 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237666 + + GSM2802299: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561394 + GSM2802299 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802299 + + + + + + + GEO Accession + GSM2802299 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561394 + SAMN07730427 + GSM2802299 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561394 + SAMN07730427 + GSM2802299 + + + + + + + SRR6125013 + GSM2802299_r1 + + + + + + SRS2561394 + SAMN07730427 + GSM2802299 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237665 + + GSM2802298: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561392 + GSM2802298 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802298 + + + + + + + GEO Accession + GSM2802298 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561392 + SAMN07730428 + GSM2802298 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561392 + SAMN07730428 + GSM2802298 + + + + + + + SRR6125012 + GSM2802298_r1 + + + + + + SRS2561392 + SAMN07730428 + GSM2802298 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237664 + + GSM2802297: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561391 + GSM2802297 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802297 + + + + + + + GEO Accession + GSM2802297 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561391 + SAMN07730429 + GSM2802297 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561391 + SAMN07730429 + GSM2802297 + + + + + + + SRR6125011 + GSM2802297_r1 + + + + + + SRS2561391 + SAMN07730429 + GSM2802297 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237663 + + GSM2802296: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561390 + GSM2802296 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802296 + + + + + + + GEO Accession + GSM2802296 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561390 + SAMN07730430 + GSM2802296 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561390 + SAMN07730430 + GSM2802296 + + + + + + + SRR6125010 + GSM2802296_r1 + + + + + + SRS2561390 + SAMN07730430 + GSM2802296 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237662 + + GSM2802295: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561389 + GSM2802295 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802295 + + + + + + + GEO Accession + GSM2802295 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561389 + SAMN07730432 + GSM2802295 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561389 + SAMN07730432 + GSM2802295 + + + + + + + SRR6125009 + GSM2802295_r1 + + + + + + SRS2561389 + SAMN07730432 + GSM2802295 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237661 + + GSM2802294: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561388 + GSM2802294 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802294 + + + + + + + GEO Accession + GSM2802294 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561388 + SAMN07730433 + GSM2802294 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561388 + SAMN07730433 + GSM2802294 + + + + + + + SRR6125008 + GSM2802294_r1 + + + + + + SRS2561388 + SAMN07730433 + GSM2802294 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237660 + + GSM2802293: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561387 + GSM2802293 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802293 + + + + + + + GEO Accession + GSM2802293 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561387 + SAMN07730434 + GSM2802293 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561387 + SAMN07730434 + GSM2802293 + + + + + + + SRR6125007 + GSM2802293_r1 + + + + + + SRS2561387 + SAMN07730434 + GSM2802293 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237659 + + GSM2802292: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561386 + GSM2802292 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802292 + + + + + + + GEO Accession + GSM2802292 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561386 + SAMN07730435 + GSM2802292 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561386 + SAMN07730435 + GSM2802292 + + + + + + + SRR6125006 + GSM2802292_r1 + + + + + + SRS2561386 + SAMN07730435 + GSM2802292 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237658 + + GSM2802291: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561385 + GSM2802291 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802291 + + + + + + + GEO Accession + GSM2802291 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561385 + SAMN07730436 + GSM2802291 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561385 + SAMN07730436 + GSM2802291 + + + + + + + SRR6125005 + GSM2802291_r1 + + + + + + SRS2561385 + SAMN07730436 + GSM2802291 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237657 + + GSM2802290: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561384 + GSM2802290 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802290 + + + + + + + GEO Accession + GSM2802290 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561384 + SAMN07730437 + GSM2802290 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561384 + SAMN07730437 + GSM2802290 + + + + + + + SRR6125004 + GSM2802290_r1 + + + + + + SRS2561384 + SAMN07730437 + GSM2802290 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237656 + + GSM2802289: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561383 + GSM2802289 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802289 + + + + + + + GEO Accession + GSM2802289 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561383 + SAMN07730438 + GSM2802289 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561383 + SAMN07730438 + GSM2802289 + + + + + + + SRR6125003 + GSM2802289_r1 + + + + + + SRS2561383 + SAMN07730438 + GSM2802289 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237655 + + GSM2802288: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561382 + GSM2802288 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802288 + + + + + + + GEO Accession + GSM2802288 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561382 + SAMN07730439 + GSM2802288 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561382 + SAMN07730439 + GSM2802288 + + + + + + + SRR6125002 + GSM2802288_r1 + + + + + + SRS2561382 + SAMN07730439 + GSM2802288 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237654 + + GSM2802287: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561381 + GSM2802287 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802287 + + + + + + + GEO Accession + GSM2802287 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561381 + SAMN07729936 + GSM2802287 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561381 + SAMN07729936 + GSM2802287 + + + + + + + SRR6125001 + GSM2802287_r1 + + + + + + SRS2561381 + SAMN07729936 + GSM2802287 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237653 + + GSM2802286: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561380 + GSM2802286 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802286 + + + + + + + GEO Accession + GSM2802286 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561380 + SAMN07729937 + GSM2802286 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561380 + SAMN07729937 + GSM2802286 + + + + + + + SRR6125000 + GSM2802286_r1 + + + + + + SRS2561380 + SAMN07729937 + GSM2802286 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237652 + + GSM2802285: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561379 + GSM2802285 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802285 + + + + + + + GEO Accession + GSM2802285 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561379 + SAMN07729938 + GSM2802285 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561379 + SAMN07729938 + GSM2802285 + + + + + + + SRR6124999 + GSM2802285_r1 + + + + + + SRS2561379 + SAMN07729938 + GSM2802285 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237651 + + GSM2802284: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561378 + GSM2802284 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802284 + + + + + + + GEO Accession + GSM2802284 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561378 + SAMN07729939 + GSM2802284 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561378 + SAMN07729939 + GSM2802284 + + + + + + + SRR6124998 + GSM2802284_r1 + + + + + + SRS2561378 + SAMN07729939 + GSM2802284 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237650 + + GSM2802283: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561377 + GSM2802283 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802283 + + + + + + + GEO Accession + GSM2802283 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561377 + SAMN07729940 + GSM2802283 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561377 + SAMN07729940 + GSM2802283 + + + + + + + SRR6124997 + GSM2802283_r1 + + + + + + SRS2561377 + SAMN07729940 + GSM2802283 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237649 + + GSM2802282: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561376 + GSM2802282 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802282 + + + + + + + GEO Accession + GSM2802282 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561376 + SAMN07729941 + GSM2802282 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561376 + SAMN07729941 + GSM2802282 + + + + + + + SRR6124996 + GSM2802282_r1 + + + + + + SRS2561376 + SAMN07729941 + GSM2802282 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237648 + + GSM2802281: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561375 + GSM2802281 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802281 + + + + + + + GEO Accession + GSM2802281 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561375 + SAMN07729942 + GSM2802281 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561375 + SAMN07729942 + GSM2802281 + + + + + + + SRR6124995 + GSM2802281_r1 + + + + + + SRS2561375 + SAMN07729942 + GSM2802281 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237647 + + GSM2802280: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561374 + GSM2802280 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802280 + + + + + + + GEO Accession + GSM2802280 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561374 + SAMN07729943 + GSM2802280 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561374 + SAMN07729943 + GSM2802280 + + + + + + + SRR6124994 + GSM2802280_r1 + + + + + + SRS2561374 + SAMN07729943 + GSM2802280 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237646 + + GSM2802279: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561373 + GSM2802279 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802279 + + + + + + + GEO Accession + GSM2802279 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561373 + SAMN07729944 + GSM2802279 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561373 + SAMN07729944 + GSM2802279 + + + + + + + SRR6124993 + GSM2802279_r1 + + + + + + SRS2561373 + SAMN07729944 + GSM2802279 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237645 + + GSM2802278: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561372 + GSM2802278 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802278 + + + + + + + GEO Accession + GSM2802278 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561372 + SAMN07729945 + GSM2802278 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561372 + SAMN07729945 + GSM2802278 + + + + + + + SRR6124992 + GSM2802278_r1 + + + + + + SRS2561372 + SAMN07729945 + GSM2802278 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237644 + + GSM2802277: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561371 + GSM2802277 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802277 + + + + + + + GEO Accession + GSM2802277 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561371 + SAMN07729946 + GSM2802277 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561371 + SAMN07729946 + GSM2802277 + + + + + + + SRR6124991 + GSM2802277_r1 + + + + + + SRS2561371 + SAMN07729946 + GSM2802277 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237643 + + GSM2802276: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561370 + GSM2802276 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802276 + + + + + + + GEO Accession + GSM2802276 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561370 + SAMN07729947 + GSM2802276 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561370 + SAMN07729947 + GSM2802276 + + + + + + + SRR6124990 + GSM2802276_r1 + + + + + + SRS2561370 + SAMN07729947 + GSM2802276 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237642 + + GSM2802275: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561369 + GSM2802275 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802275 + + + + + + + GEO Accession + GSM2802275 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561369 + SAMN07729948 + GSM2802275 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561369 + SAMN07729948 + GSM2802275 + + + + + + + SRR6124989 + GSM2802275_r1 + + + + + + SRS2561369 + SAMN07729948 + GSM2802275 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237641 + + GSM2802274: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561368 + GSM2802274 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802274 + + + + + + + GEO Accession + GSM2802274 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561368 + SAMN07729949 + GSM2802274 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561368 + SAMN07729949 + GSM2802274 + + + + + + + SRR6124988 + GSM2802274_r1 + + + + + + SRS2561368 + SAMN07729949 + GSM2802274 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237640 + + GSM2802273: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561367 + GSM2802273 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802273 + + + + + + + GEO Accession + GSM2802273 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561367 + SAMN07729950 + GSM2802273 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561367 + SAMN07729950 + GSM2802273 + + + + + + + SRR6124987 + GSM2802273_r1 + + + + + + SRS2561367 + SAMN07729950 + GSM2802273 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237639 + + GSM2802272: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561366 + GSM2802272 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802272 + + + + + + + GEO Accession + GSM2802272 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561366 + SAMN07729956 + GSM2802272 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561366 + SAMN07729956 + GSM2802272 + + + + + + + SRR6124986 + GSM2802272_r1 + + + + + + SRS2561366 + SAMN07729956 + GSM2802272 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237638 + + GSM2802271: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561365 + GSM2802271 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802271 + + + + + + + GEO Accession + GSM2802271 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561365 + SAMN07729951 + GSM2802271 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561365 + SAMN07729951 + GSM2802271 + + + + + + + SRR6124985 + GSM2802271_r1 + + + + + + SRS2561365 + SAMN07729951 + GSM2802271 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237637 + + GSM2802270: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561364 + GSM2802270 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802270 + + + + + + + GEO Accession + GSM2802270 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561364 + SAMN07729952 + GSM2802270 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561364 + SAMN07729952 + GSM2802270 + + + + + + + SRR6124984 + GSM2802270_r1 + + + + + + SRS2561364 + SAMN07729952 + GSM2802270 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237636 + + GSM2802269: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561363 + GSM2802269 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802269 + + + + + + + GEO Accession + GSM2802269 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561363 + SAMN07729953 + GSM2802269 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561363 + SAMN07729953 + GSM2802269 + + + + + + + SRR6124983 + GSM2802269_r1 + + + + + + SRS2561363 + SAMN07729953 + GSM2802269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237635 + + GSM2802268: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561362 + GSM2802268 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802268 + + + + + + + GEO Accession + GSM2802268 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561362 + SAMN07729954 + GSM2802268 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561362 + SAMN07729954 + GSM2802268 + + + + + + + SRR6124982 + GSM2802268_r1 + + + + + + SRS2561362 + SAMN07729954 + GSM2802268 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237634 + + GSM2802267: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561361 + GSM2802267 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802267 + + + + + + + GEO Accession + GSM2802267 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561361 + SAMN07729955 + GSM2802267 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561361 + SAMN07729955 + GSM2802267 + + + + + + + SRR6124981 + GSM2802267_r1 + + + + + + SRS2561361 + SAMN07729955 + GSM2802267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237633 + + GSM2802266: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561360 + GSM2802266 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802266 + + + + + + + GEO Accession + GSM2802266 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561360 + SAMN07729957 + GSM2802266 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561360 + SAMN07729957 + GSM2802266 + + + + + + + SRR6124980 + GSM2802266_r1 + + + + + + SRS2561360 + SAMN07729957 + GSM2802266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237632 + + GSM2802265: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561359 + GSM2802265 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802265 + + + + + + + GEO Accession + GSM2802265 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561359 + SAMN07729958 + GSM2802265 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561359 + SAMN07729958 + GSM2802265 + + + + + + + SRR6124979 + GSM2802265_r1 + + + + + + SRS2561359 + SAMN07729958 + GSM2802265 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237631 + + GSM2802264: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561358 + GSM2802264 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802264 + + + + + + + GEO Accession + GSM2802264 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561358 + SAMN07729959 + GSM2802264 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561358 + SAMN07729959 + GSM2802264 + + + + + + + SRR6124978 + GSM2802264_r1 + + + + + + SRS2561358 + SAMN07729959 + GSM2802264 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237630 + + GSM2802263: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561357 + GSM2802263 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802263 + + + + + + + GEO Accession + GSM2802263 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561357 + SAMN07729960 + GSM2802263 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561357 + SAMN07729960 + GSM2802263 + + + + + + + SRR6124977 + GSM2802263_r1 + + + + + + SRS2561357 + SAMN07729960 + GSM2802263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237629 + + GSM2802262: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561356 + GSM2802262 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802262 + + + + + + + GEO Accession + GSM2802262 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561356 + SAMN07729961 + GSM2802262 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561356 + SAMN07729961 + GSM2802262 + + + + + + + SRR6124976 + GSM2802262_r1 + + + + + + SRS2561356 + SAMN07729961 + GSM2802262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237628 + + GSM2802261: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561355 + GSM2802261 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802261 + + + + + + + GEO Accession + GSM2802261 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561355 + SAMN07729962 + GSM2802261 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561355 + SAMN07729962 + GSM2802261 + + + + + + + SRR6124975 + GSM2802261_r1 + + + + + + SRS2561355 + SAMN07729962 + GSM2802261 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237627 + + GSM2802260: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561354 + GSM2802260 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802260 + + + + + + + GEO Accession + GSM2802260 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561354 + SAMN07729821 + GSM2802260 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561354 + SAMN07729821 + GSM2802260 + + + + + + + SRR6124974 + GSM2802260_r1 + + + + + + SRS2561354 + SAMN07729821 + GSM2802260 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237626 + + GSM2802259: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561353 + GSM2802259 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802259 + + + + + + + GEO Accession + GSM2802259 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561353 + SAMN07729822 + GSM2802259 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561353 + SAMN07729822 + GSM2802259 + + + + + + + SRR6124973 + GSM2802259_r1 + + + + + + SRS2561353 + SAMN07729822 + GSM2802259 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237625 + + GSM2802258: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561352 + GSM2802258 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802258 + + + + + + + GEO Accession + GSM2802258 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561352 + SAMN07729823 + GSM2802258 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561352 + SAMN07729823 + GSM2802258 + + + + + + + SRR6124972 + GSM2802258_r1 + + + + + + SRS2561352 + SAMN07729823 + GSM2802258 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237624 + + GSM2802257: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561351 + GSM2802257 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802257 + + + + + + + GEO Accession + GSM2802257 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561351 + SAMN07730530 + GSM2802257 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561351 + SAMN07730530 + GSM2802257 + + + + + + + SRR6124971 + GSM2802257_r1 + + + + + + SRS2561351 + SAMN07730530 + GSM2802257 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237623 + + GSM2802256: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561350 + GSM2802256 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802256 + + + + + + + GEO Accession + GSM2802256 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561350 + SAMN07730531 + GSM2802256 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561350 + SAMN07730531 + GSM2802256 + + + + + + + SRR6124970 + GSM2802256_r1 + + + + + + SRS2561350 + SAMN07730531 + GSM2802256 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237622 + + GSM2802255: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561348 + GSM2802255 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802255 + + + + + + + GEO Accession + GSM2802255 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561348 + SAMN07730532 + GSM2802255 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561348 + SAMN07730532 + GSM2802255 + + + + + + + SRR6124969 + GSM2802255_r1 + + + + + + SRS2561348 + SAMN07730532 + GSM2802255 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237621 + + GSM2802254: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561349 + GSM2802254 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802254 + + + + + + + GEO Accession + GSM2802254 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561349 + SAMN07730533 + GSM2802254 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561349 + SAMN07730533 + GSM2802254 + + + + + + + SRR6124968 + GSM2802254_r1 + + + + + + SRS2561349 + SAMN07730533 + GSM2802254 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237620 + + GSM2802253: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561347 + GSM2802253 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802253 + + + + + + + GEO Accession + GSM2802253 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561347 + SAMN07730534 + GSM2802253 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561347 + SAMN07730534 + GSM2802253 + + + + + + + SRR6124967 + GSM2802253_r1 + + + + + + SRS2561347 + SAMN07730534 + GSM2802253 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237619 + + GSM2802252: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561346 + GSM2802252 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802252 + + + + + + + GEO Accession + GSM2802252 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561346 + SAMN07730535 + GSM2802252 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561346 + SAMN07730535 + GSM2802252 + + + + + + + SRR6124966 + GSM2802252_r1 + + + + + + SRS2561346 + SAMN07730535 + GSM2802252 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237618 + + GSM2802251: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561344 + GSM2802251 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802251 + + + + + + + GEO Accession + GSM2802251 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561344 + SAMN07730536 + GSM2802251 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561344 + SAMN07730536 + GSM2802251 + + + + + + + SRR6124965 + GSM2802251_r1 + + + + + + SRS2561344 + SAMN07730536 + GSM2802251 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237617 + + GSM2802250: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561345 + GSM2802250 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802250 + + + + + + + GEO Accession + GSM2802250 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561345 + SAMN07730537 + GSM2802250 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561345 + SAMN07730537 + GSM2802250 + + + + + + + SRR6124964 + GSM2802250_r1 + + + + + + SRS2561345 + SAMN07730537 + GSM2802250 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237616 + + GSM2802249: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561342 + GSM2802249 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802249 + + + + + + + GEO Accession + GSM2802249 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561342 + SAMN07730538 + GSM2802249 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561342 + SAMN07730538 + GSM2802249 + + + + + + + SRR6124963 + GSM2802249_r1 + + + + + + SRS2561342 + SAMN07730538 + GSM2802249 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237615 + + GSM2802248: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561343 + GSM2802248 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802248 + + + + + + + GEO Accession + GSM2802248 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561343 + SAMN07730539 + GSM2802248 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561343 + SAMN07730539 + GSM2802248 + + + + + + + SRR6124962 + GSM2802248_r1 + + + + + + SRS2561343 + SAMN07730539 + GSM2802248 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237614 + + GSM2802247: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561341 + GSM2802247 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802247 + + + + + + + GEO Accession + GSM2802247 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561341 + SAMN07730540 + GSM2802247 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561341 + SAMN07730540 + GSM2802247 + + + + + + + SRR6124961 + GSM2802247_r1 + + + + + + SRS2561341 + SAMN07730540 + GSM2802247 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237613 + + GSM2802246: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561340 + GSM2802246 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802246 + + + + + + + GEO Accession + GSM2802246 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561340 + SAMN07730541 + GSM2802246 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561340 + SAMN07730541 + GSM2802246 + + + + + + + SRR6124960 + GSM2802246_r1 + + + + + + SRS2561340 + SAMN07730541 + GSM2802246 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237612 + + GSM2802245: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561338 + GSM2802245 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802245 + + + + + + + GEO Accession + GSM2802245 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561338 + SAMN07730542 + GSM2802245 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561338 + SAMN07730542 + GSM2802245 + + + + + + + SRR6124959 + GSM2802245_r1 + + + + + + SRS2561338 + SAMN07730542 + GSM2802245 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237611 + + GSM2802244: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561339 + GSM2802244 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802244 + + + + + + + GEO Accession + GSM2802244 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561339 + SAMN07730543 + GSM2802244 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561339 + SAMN07730543 + GSM2802244 + + + + + + + SRR6124958 + GSM2802244_r1 + + + + + + SRS2561339 + SAMN07730543 + GSM2802244 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237610 + + GSM2802243: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561337 + GSM2802243 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802243 + + + + + + + GEO Accession + GSM2802243 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561337 + SAMN07730544 + GSM2802243 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561337 + SAMN07730544 + GSM2802243 + + + + + + + SRR6124957 + GSM2802243_r1 + + + + + + SRS2561337 + SAMN07730544 + GSM2802243 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237609 + + GSM2802242: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561336 + GSM2802242 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802242 + + + + + + + GEO Accession + GSM2802242 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561336 + SAMN07730545 + GSM2802242 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561336 + SAMN07730545 + GSM2802242 + + + + + + + SRR6124956 + GSM2802242_r1 + + + + + + SRS2561336 + SAMN07730545 + GSM2802242 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237608 + + GSM2802241: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561335 + GSM2802241 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802241 + + + + + + + GEO Accession + GSM2802241 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561335 + SAMN07730546 + GSM2802241 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561335 + SAMN07730546 + GSM2802241 + + + + + + + SRR6124955 + GSM2802241_r1 + + + + + + SRS2561335 + SAMN07730546 + GSM2802241 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237607 + + GSM2802240: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561334 + GSM2802240 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802240 + + + + + + + GEO Accession + GSM2802240 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561334 + SAMN07730547 + GSM2802240 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561334 + SAMN07730547 + GSM2802240 + + + + + + + SRR6124954 + GSM2802240_r1 + + + + + + SRS2561334 + SAMN07730547 + GSM2802240 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237606 + + GSM2802239: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561333 + GSM2802239 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802239 + + + + + + + GEO Accession + GSM2802239 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561333 + SAMN07730548 + GSM2802239 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561333 + SAMN07730548 + GSM2802239 + + + + + + + SRR6124953 + GSM2802239_r1 + + + + + + SRS2561333 + SAMN07730548 + GSM2802239 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237605 + + GSM2802238: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561332 + GSM2802238 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802238 + + + + + + + GEO Accession + GSM2802238 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561332 + SAMN07730549 + GSM2802238 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561332 + SAMN07730549 + GSM2802238 + + + + + + + SRR6124952 + GSM2802238_r1 + + + + + + SRS2561332 + SAMN07730549 + GSM2802238 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237604 + + GSM2802237: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561331 + GSM2802237 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802237 + + + + + + + GEO Accession + GSM2802237 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561331 + SAMN07730550 + GSM2802237 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561331 + SAMN07730550 + GSM2802237 + + + + + + + SRR6124951 + GSM2802237_r1 + + + + + + SRS2561331 + SAMN07730550 + GSM2802237 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237603 + + GSM2802236: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561330 + GSM2802236 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802236 + + + + + + + GEO Accession + GSM2802236 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561330 + SAMN07730551 + GSM2802236 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561330 + SAMN07730551 + GSM2802236 + + + + + + + SRR6124950 + GSM2802236_r1 + + + + + + SRS2561330 + SAMN07730551 + GSM2802236 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237602 + + GSM2802235: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561329 + GSM2802235 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802235 + + + + + + + GEO Accession + GSM2802235 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561329 + SAMN07730552 + GSM2802235 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561329 + SAMN07730552 + GSM2802235 + + + + + + + SRR6124949 + GSM2802235_r1 + + + + + + SRS2561329 + SAMN07730552 + GSM2802235 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237601 + + GSM2802234: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561328 + GSM2802234 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802234 + + + + + + + GEO Accession + GSM2802234 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561328 + SAMN07730553 + GSM2802234 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561328 + SAMN07730553 + GSM2802234 + + + + + + + SRR6124948 + GSM2802234_r1 + + + + + + SRS2561328 + SAMN07730553 + GSM2802234 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237600 + + GSM2802233: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561327 + GSM2802233 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802233 + + + + + + + GEO Accession + GSM2802233 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561327 + SAMN07730554 + GSM2802233 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561327 + SAMN07730554 + GSM2802233 + + + + + + + SRR6124947 + GSM2802233_r1 + + + + + + SRS2561327 + SAMN07730554 + GSM2802233 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237599 + + GSM2802232: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561326 + GSM2802232 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802232 + + + + + + + GEO Accession + GSM2802232 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561326 + SAMN07730555 + GSM2802232 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561326 + SAMN07730555 + GSM2802232 + + + + + + + SRR6124946 + GSM2802232_r1 + + + + + + SRS2561326 + SAMN07730555 + GSM2802232 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237598 + + GSM2802231: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561325 + GSM2802231 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802231 + + + + + + + GEO Accession + GSM2802231 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561325 + SAMN07730556 + GSM2802231 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561325 + SAMN07730556 + GSM2802231 + + + + + + + SRR6124945 + GSM2802231_r1 + + + + + + SRS2561325 + SAMN07730556 + GSM2802231 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237597 + + GSM2802230: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561324 + GSM2802230 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802230 + + + + + + + GEO Accession + GSM2802230 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561324 + SAMN07730557 + GSM2802230 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561324 + SAMN07730557 + GSM2802230 + + + + + + + SRR6124944 + GSM2802230_r1 + + + + + + SRS2561324 + SAMN07730557 + GSM2802230 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237596 + + GSM2802229: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561323 + GSM2802229 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802229 + + + + + + + GEO Accession + GSM2802229 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561323 + SAMN07730558 + GSM2802229 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561323 + SAMN07730558 + GSM2802229 + + + + + + + SRR6124943 + GSM2802229_r1 + + + + + + SRS2561323 + SAMN07730558 + GSM2802229 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237595 + + GSM2802228: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561322 + GSM2802228 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802228 + + + + + + + GEO Accession + GSM2802228 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561322 + SAMN07730559 + GSM2802228 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561322 + SAMN07730559 + GSM2802228 + + + + + + + SRR6124942 + GSM2802228_r1 + + + + + + SRS2561322 + SAMN07730559 + GSM2802228 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237594 + + GSM2802227: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561321 + GSM2802227 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802227 + + + + + + + GEO Accession + GSM2802227 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561321 + SAMN07730243 + GSM2802227 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561321 + SAMN07730243 + GSM2802227 + + + + + + + SRR6124941 + GSM2802227_r1 + + + + + + SRS2561321 + SAMN07730243 + GSM2802227 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237593 + + GSM2802226: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561320 + GSM2802226 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802226 + + + + + + + GEO Accession + GSM2802226 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561320 + SAMN07730244 + GSM2802226 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561320 + SAMN07730244 + GSM2802226 + + + + + + + SRR6124940 + GSM2802226_r1 + + + + + + SRS2561320 + SAMN07730244 + GSM2802226 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237592 + + GSM2802225: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561319 + GSM2802225 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802225 + + + + + + + GEO Accession + GSM2802225 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561319 + SAMN07730245 + GSM2802225 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561319 + SAMN07730245 + GSM2802225 + + + + + + + SRR6124939 + GSM2802225_r1 + + + + + + SRS2561319 + SAMN07730245 + GSM2802225 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237591 + + GSM2802224: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561318 + GSM2802224 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802224 + + + + + + + GEO Accession + GSM2802224 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561318 + SAMN07730246 + GSM2802224 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561318 + SAMN07730246 + GSM2802224 + + + + + + + SRR6124938 + GSM2802224_r1 + + + + + + SRS2561318 + SAMN07730246 + GSM2802224 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237590 + + GSM2802223: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561317 + GSM2802223 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802223 + + + + + + + GEO Accession + GSM2802223 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561317 + SAMN07730247 + GSM2802223 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561317 + SAMN07730247 + GSM2802223 + + + + + + + SRR6124937 + GSM2802223_r1 + + + + + + SRS2561317 + SAMN07730247 + GSM2802223 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237589 + + GSM2802222: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561316 + GSM2802222 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802222 + + + + + + + GEO Accession + GSM2802222 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561316 + SAMN07730248 + GSM2802222 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561316 + SAMN07730248 + GSM2802222 + + + + + + + SRR6124936 + GSM2802222_r1 + + + + + + SRS2561316 + SAMN07730248 + GSM2802222 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237588 + + GSM2802221: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561315 + GSM2802221 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802221 + + + + + + + GEO Accession + GSM2802221 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561315 + SAMN07730249 + GSM2802221 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561315 + SAMN07730249 + GSM2802221 + + + + + + + SRR6124935 + GSM2802221_r1 + + + + + + SRS2561315 + SAMN07730249 + GSM2802221 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237587 + + GSM2802220: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561313 + GSM2802220 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802220 + + + + + + + GEO Accession + GSM2802220 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561313 + SAMN07730250 + GSM2802220 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561313 + SAMN07730250 + GSM2802220 + + + + + + + SRR6124934 + GSM2802220_r1 + + + + + + SRS2561313 + SAMN07730250 + GSM2802220 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237586 + + GSM2802219: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561314 + GSM2802219 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802219 + + + + + + + GEO Accession + GSM2802219 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561314 + SAMN07730251 + GSM2802219 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561314 + SAMN07730251 + GSM2802219 + + + + + + + SRR6124933 + GSM2802219_r1 + + + + + + SRS2561314 + SAMN07730251 + GSM2802219 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237585 + + GSM2802218: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561312 + GSM2802218 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802218 + + + + + + + GEO Accession + GSM2802218 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561312 + SAMN07730252 + GSM2802218 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561312 + SAMN07730252 + GSM2802218 + + + + + + + SRR6124932 + GSM2802218_r1 + + + + + + SRS2561312 + SAMN07730252 + GSM2802218 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237584 + + GSM2802217: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561309 + GSM2802217 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802217 + + + + + + + GEO Accession + GSM2802217 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561309 + SAMN07730253 + GSM2802217 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561309 + SAMN07730253 + GSM2802217 + + + + + + + SRR6124931 + GSM2802217_r1 + + + + + + SRS2561309 + SAMN07730253 + GSM2802217 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237583 + + GSM2802216: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561311 + GSM2802216 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802216 + + + + + + + GEO Accession + GSM2802216 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561311 + SAMN07730254 + GSM2802216 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561311 + SAMN07730254 + GSM2802216 + + + + + + + SRR6124930 + GSM2802216_r1 + + + + + + SRS2561311 + SAMN07730254 + GSM2802216 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237582 + + GSM2802215: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561310 + GSM2802215 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802215 + + + + + + + GEO Accession + GSM2802215 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561310 + SAMN07730255 + GSM2802215 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561310 + SAMN07730255 + GSM2802215 + + + + + + + SRR6124929 + GSM2802215_r1 + + + + + + SRS2561310 + SAMN07730255 + GSM2802215 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237581 + + GSM2802214: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561308 + GSM2802214 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802214 + + + + + + + GEO Accession + GSM2802214 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561308 + SAMN07730256 + GSM2802214 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561308 + SAMN07730256 + GSM2802214 + + + + + + + SRR6124928 + GSM2802214_r1 + + + + + + SRS2561308 + SAMN07730256 + GSM2802214 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237580 + + GSM2802213: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561306 + GSM2802213 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802213 + + + + + + + GEO Accession + GSM2802213 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561306 + SAMN07730257 + GSM2802213 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561306 + SAMN07730257 + GSM2802213 + + + + + + + SRR6124927 + GSM2802213_r1 + + + + + + SRS2561306 + SAMN07730257 + GSM2802213 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237579 + + GSM2802212: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561307 + GSM2802212 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802212 + + + + + + + GEO Accession + GSM2802212 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561307 + SAMN07730258 + GSM2802212 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561307 + SAMN07730258 + GSM2802212 + + + + + + + SRR6124926 + GSM2802212_r1 + + + + + + SRS2561307 + SAMN07730258 + GSM2802212 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237578 + + GSM2802211: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561305 + GSM2802211 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802211 + + + + + + + GEO Accession + GSM2802211 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561305 + SAMN07730259 + GSM2802211 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561305 + SAMN07730259 + GSM2802211 + + + + + + + SRR6124925 + GSM2802211_r1 + + + + + + SRS2561305 + SAMN07730259 + GSM2802211 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237577 + + GSM2802210: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561304 + GSM2802210 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802210 + + + + + + + GEO Accession + GSM2802210 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561304 + SAMN07730260 + GSM2802210 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561304 + SAMN07730260 + GSM2802210 + + + + + + + SRR6124924 + GSM2802210_r1 + + + + + + SRS2561304 + SAMN07730260 + GSM2802210 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237576 + + GSM2802209: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561303 + GSM2802209 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802209 + + + + + + + GEO Accession + GSM2802209 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561303 + SAMN07730261 + GSM2802209 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561303 + SAMN07730261 + GSM2802209 + + + + + + + SRR6124923 + GSM2802209_r1 + + + + + + SRS2561303 + SAMN07730261 + GSM2802209 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237575 + + GSM2802208: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561302 + GSM2802208 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802208 + + + + + + + GEO Accession + GSM2802208 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561302 + SAMN07730262 + GSM2802208 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561302 + SAMN07730262 + GSM2802208 + + + + + + + SRR6124922 + GSM2802208_r1 + + + + + + SRS2561302 + SAMN07730262 + GSM2802208 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237574 + + GSM2802207: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561301 + GSM2802207 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802207 + + + + + + + GEO Accession + GSM2802207 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561301 + SAMN07729875 + GSM2802207 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561301 + SAMN07729875 + GSM2802207 + + + + + + + SRR6124921 + GSM2802207_r1 + + + + + + SRS2561301 + SAMN07729875 + GSM2802207 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237573 + + GSM2802206: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561300 + GSM2802206 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802206 + + + + + + + GEO Accession + GSM2802206 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561300 + SAMN07729876 + GSM2802206 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561300 + SAMN07729876 + GSM2802206 + + + + + + + SRR6124920 + GSM2802206_r1 + + + + + + SRS2561300 + SAMN07729876 + GSM2802206 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237572 + + GSM2802205: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561299 + GSM2802205 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802205 + + + + + + + GEO Accession + GSM2802205 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561299 + SAMN07729877 + GSM2802205 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561299 + SAMN07729877 + GSM2802205 + + + + + + + SRR6124919 + GSM2802205_r1 + + + + + + SRS2561299 + SAMN07729877 + GSM2802205 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237571 + + GSM2802204: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561298 + GSM2802204 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802204 + + + + + + + GEO Accession + GSM2802204 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561298 + SAMN07729878 + GSM2802204 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561298 + SAMN07729878 + GSM2802204 + + + + + + + SRR6124918 + GSM2802204_r1 + + + + + + SRS2561298 + SAMN07729878 + GSM2802204 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237570 + + GSM2802203: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561296 + GSM2802203 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802203 + + + + + + + GEO Accession + GSM2802203 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561296 + SAMN07730353 + GSM2802203 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561296 + SAMN07730353 + GSM2802203 + + + + + + + SRR6124917 + GSM2802203_r1 + + + + + + SRS2561296 + SAMN07730353 + GSM2802203 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237569 + + GSM2802202: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561297 + GSM2802202 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802202 + + + + + + + GEO Accession + GSM2802202 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561297 + SAMN07730354 + GSM2802202 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561297 + SAMN07730354 + GSM2802202 + + + + + + + SRR6124916 + GSM2802202_r1 + + + + + + SRS2561297 + SAMN07730354 + GSM2802202 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237568 + + GSM2802201: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561295 + GSM2802201 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802201 + + + + + + + GEO Accession + GSM2802201 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561295 + SAMN07730355 + GSM2802201 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561295 + SAMN07730355 + GSM2802201 + + + + + + + SRR6124915 + GSM2802201_r1 + + + + + + SRS2561295 + SAMN07730355 + GSM2802201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237567 + + GSM2802200: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561293 + GSM2802200 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802200 + + + + + + + GEO Accession + GSM2802200 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561293 + SAMN07730356 + GSM2802200 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561293 + SAMN07730356 + GSM2802200 + + + + + + + SRR6124914 + GSM2802200_r1 + + + + + + SRS2561293 + SAMN07730356 + GSM2802200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237566 + + GSM2802199: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561294 + GSM2802199 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802199 + + + + + + + GEO Accession + GSM2802199 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561294 + SAMN07730357 + GSM2802199 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561294 + SAMN07730357 + GSM2802199 + + + + + + + SRR6124913 + GSM2802199_r1 + + + + + + SRS2561294 + SAMN07730357 + GSM2802199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237565 + + GSM2802198: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561292 + GSM2802198 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802198 + + + + + + + GEO Accession + GSM2802198 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561292 + SAMN07730358 + GSM2802198 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561292 + SAMN07730358 + GSM2802198 + + + + + + + SRR6124912 + GSM2802198_r1 + + + + + + SRS2561292 + SAMN07730358 + GSM2802198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237564 + + GSM2802197: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561290 + GSM2802197 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802197 + + + + + + + GEO Accession + GSM2802197 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561290 + SAMN07730359 + GSM2802197 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561290 + SAMN07730359 + GSM2802197 + + + + + + + SRR6124911 + GSM2802197_r1 + + + + + + SRS2561290 + SAMN07730359 + GSM2802197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237563 + + GSM2802196: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561291 + GSM2802196 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802196 + + + + + + + GEO Accession + GSM2802196 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561291 + SAMN07730360 + GSM2802196 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561291 + SAMN07730360 + GSM2802196 + + + + + + + SRR6124910 + GSM2802196_r1 + + + + + + SRS2561291 + SAMN07730360 + GSM2802196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237562 + + GSM2802195: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561289 + GSM2802195 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802195 + + + + + + + GEO Accession + GSM2802195 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561289 + SAMN07730361 + GSM2802195 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561289 + SAMN07730361 + GSM2802195 + + + + + + + SRR6124909 + GSM2802195_r1 + + + + + + SRS2561289 + SAMN07730361 + GSM2802195 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237561 + + GSM2802194: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561287 + GSM2802194 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802194 + + + + + + + GEO Accession + GSM2802194 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561287 + SAMN07730362 + GSM2802194 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561287 + SAMN07730362 + GSM2802194 + + + + + + + SRR6124908 + GSM2802194_r1 + + + + + + SRS2561287 + SAMN07730362 + GSM2802194 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237560 + + GSM2802193: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561288 + GSM2802193 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802193 + + + + + + + GEO Accession + GSM2802193 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561288 + SAMN07730363 + GSM2802193 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561288 + SAMN07730363 + GSM2802193 + + + + + + + SRR6124907 + GSM2802193_r1 + + + + + + SRS2561288 + SAMN07730363 + GSM2802193 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237559 + + GSM2802192: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561286 + GSM2802192 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802192 + + + + + + + GEO Accession + GSM2802192 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561286 + SAMN07730364 + GSM2802192 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561286 + SAMN07730364 + GSM2802192 + + + + + + + SRR6124906 + GSM2802192_r1 + + + + + + SRS2561286 + SAMN07730364 + GSM2802192 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237558 + + GSM2802191: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561285 + GSM2802191 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802191 + + + + + + + GEO Accession + GSM2802191 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561285 + SAMN07730365 + GSM2802191 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561285 + SAMN07730365 + GSM2802191 + + + + + + + SRR6124905 + GSM2802191_r1 + + + + + + SRS2561285 + SAMN07730365 + GSM2802191 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237557 + + GSM2802190: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561284 + GSM2802190 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802190 + + + + + + + GEO Accession + GSM2802190 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561284 + SAMN07730366 + GSM2802190 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561284 + SAMN07730366 + GSM2802190 + + + + + + + SRR6124904 + GSM2802190_r1 + + + + + + SRS2561284 + SAMN07730366 + GSM2802190 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237556 + + GSM2802189: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561283 + GSM2802189 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802189 + + + + + + + GEO Accession + GSM2802189 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561283 + SAMN07730367 + GSM2802189 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561283 + SAMN07730367 + GSM2802189 + + + + + + + SRR6124903 + GSM2802189_r1 + + + + + + SRS2561283 + SAMN07730367 + GSM2802189 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237555 + + GSM2802188: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561282 + GSM2802188 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802188 + + + + + + + GEO Accession + GSM2802188 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561282 + SAMN07730368 + GSM2802188 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561282 + SAMN07730368 + GSM2802188 + + + + + + + SRR6124902 + GSM2802188_r1 + + + + + + SRS2561282 + SAMN07730368 + GSM2802188 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237554 + + GSM2802187: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561281 + GSM2802187 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802187 + + + + + + + GEO Accession + GSM2802187 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561281 + SAMN07730369 + GSM2802187 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561281 + SAMN07730369 + GSM2802187 + + + + + + + SRR6124901 + GSM2802187_r1 + + + + + + SRS2561281 + SAMN07730369 + GSM2802187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237553 + + GSM2802186: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561280 + GSM2802186 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802186 + + + + + + + GEO Accession + GSM2802186 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561280 + SAMN07730370 + GSM2802186 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561280 + SAMN07730370 + GSM2802186 + + + + + + + SRR6124900 + GSM2802186_r1 + + + + + + SRS2561280 + SAMN07730370 + GSM2802186 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237552 + + GSM2802185: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561277 + GSM2802185 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802185 + + + + + + + GEO Accession + GSM2802185 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561277 + SAMN07730371 + GSM2802185 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561277 + SAMN07730371 + GSM2802185 + + + + + + + SRR6124899 + GSM2802185_r1 + + + + + + SRS2561277 + SAMN07730371 + GSM2802185 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237551 + + GSM2802184: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561278 + GSM2802184 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802184 + + + + + + + GEO Accession + GSM2802184 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561278 + SAMN07730377 + GSM2802184 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561278 + SAMN07730377 + GSM2802184 + + + + + + + SRR6124898 + GSM2802184_r1 + + + + + + SRS2561278 + SAMN07730377 + GSM2802184 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237550 + + GSM2802183: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561279 + GSM2802183 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802183 + + + + + + + GEO Accession + GSM2802183 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561279 + SAMN07730378 + GSM2802183 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561279 + SAMN07730378 + GSM2802183 + + + + + + + SRR6124897 + GSM2802183_r1 + + + + + + SRS2561279 + SAMN07730378 + GSM2802183 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237549 + + GSM2802182: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561275 + GSM2802182 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802182 + + + + + + + GEO Accession + GSM2802182 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561275 + SAMN07730379 + GSM2802182 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561275 + SAMN07730379 + GSM2802182 + + + + + + + SRR6124896 + GSM2802182_r1 + + + + + + SRS2561275 + SAMN07730379 + GSM2802182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237548 + + GSM2802181: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561274 + GSM2802181 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802181 + + + + + + + GEO Accession + GSM2802181 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561274 + SAMN07730372 + GSM2802181 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561274 + SAMN07730372 + GSM2802181 + + + + + + + SRR6124895 + GSM2802181_r1 + + + + + + SRS2561274 + SAMN07730372 + GSM2802181 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237547 + + GSM2802180: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561276 + GSM2802180 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802180 + + + + + + + GEO Accession + GSM2802180 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561276 + SAMN07730373 + GSM2802180 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561276 + SAMN07730373 + GSM2802180 + + + + + + + SRR6124894 + GSM2802180_r1 + + + + + + SRS2561276 + SAMN07730373 + GSM2802180 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237546 + + GSM2802179: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561273 + GSM2802179 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802179 + + + + + + + GEO Accession + GSM2802179 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561273 + SAMN07730374 + GSM2802179 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561273 + SAMN07730374 + GSM2802179 + + + + + + + SRR6124893 + GSM2802179_r1 + + + + + + SRS2561273 + SAMN07730374 + GSM2802179 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237545 + + GSM2802178: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561272 + GSM2802178 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802178 + + + + + + + GEO Accession + GSM2802178 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561272 + SAMN07730375 + GSM2802178 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561272 + SAMN07730375 + GSM2802178 + + + + + + + SRR6124892 + GSM2802178_r1 + + + + + + SRS2561272 + SAMN07730375 + GSM2802178 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237544 + + GSM2802177: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561271 + GSM2802177 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802177 + + + + + + + GEO Accession + GSM2802177 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561271 + SAMN07730376 + GSM2802177 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561271 + SAMN07730376 + GSM2802177 + + + + + + + SRR6124891 + GSM2802177_r1 + + + + + + SRS2561271 + SAMN07730376 + GSM2802177 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237543 + + GSM2802176: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561270 + GSM2802176 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802176 + + + + + + + GEO Accession + GSM2802176 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561270 + SAMN07730380 + GSM2802176 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561270 + SAMN07730380 + GSM2802176 + + + + + + + SRR6124890 + GSM2802176_r1 + + + + + + SRS2561270 + SAMN07730380 + GSM2802176 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237542 + + GSM2802175: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561269 + GSM2802175 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802175 + + + + + + + GEO Accession + GSM2802175 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561269 + SAMN07730381 + GSM2802175 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561269 + SAMN07730381 + GSM2802175 + + + + + + + SRR6124889 + GSM2802175_r1 + + + + + + SRS2561269 + SAMN07730381 + GSM2802175 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237541 + + GSM2802174: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561268 + GSM2802174 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802174 + + + + + + + GEO Accession + GSM2802174 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561268 + SAMN07730382 + GSM2802174 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561268 + SAMN07730382 + GSM2802174 + + + + + + + SRR6124888 + GSM2802174_r1 + + + + + + SRS2561268 + SAMN07730382 + GSM2802174 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237540 + + GSM2802173: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561267 + GSM2802173 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802173 + + + + + + + GEO Accession + GSM2802173 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561267 + SAMN07730404 + GSM2802173 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561267 + SAMN07730404 + GSM2802173 + + + + + + + SRR6124887 + GSM2802173_r1 + + + + + + SRS2561267 + SAMN07730404 + GSM2802173 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237539 + + GSM2802172: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561266 + GSM2802172 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802172 + + + + + + + GEO Accession + GSM2802172 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561266 + SAMN07730405 + GSM2802172 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561266 + SAMN07730405 + GSM2802172 + + + + + + + SRR6124886 + GSM2802172_r1 + + + + + + SRS2561266 + SAMN07730405 + GSM2802172 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237538 + + GSM2802171: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561265 + GSM2802171 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802171 + + + + + + + GEO Accession + GSM2802171 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561265 + SAMN07730406 + GSM2802171 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561265 + SAMN07730406 + GSM2802171 + + + + + + + SRR6124885 + GSM2802171_r1 + + + + + + SRS2561265 + SAMN07730406 + GSM2802171 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237537 + + GSM2802170: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561264 + GSM2802170 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802170 + + + + + + + GEO Accession + GSM2802170 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561264 + SAMN07730407 + GSM2802170 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561264 + SAMN07730407 + GSM2802170 + + + + + + + SRR6124884 + GSM2802170_r1 + + + + + + SRS2561264 + SAMN07730407 + GSM2802170 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237536 + + GSM2802169: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561263 + GSM2802169 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802169 + + + + + + + GEO Accession + GSM2802169 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561263 + SAMN07730408 + GSM2802169 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561263 + SAMN07730408 + GSM2802169 + + + + + + + SRR6124883 + GSM2802169_r1 + + + + + + SRS2561263 + SAMN07730408 + GSM2802169 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237535 + + GSM2802168: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561262 + GSM2802168 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802168 + + + + + + + GEO Accession + GSM2802168 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561262 + SAMN07730409 + GSM2802168 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561262 + SAMN07730409 + GSM2802168 + + + + + + + SRR6124882 + GSM2802168_r1 + + + + + + SRS2561262 + SAMN07730409 + GSM2802168 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237534 + + GSM2802167: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561261 + GSM2802167 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802167 + + + + + + + GEO Accession + GSM2802167 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561261 + SAMN07730383 + GSM2802167 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561261 + SAMN07730383 + GSM2802167 + + + + + + + SRR6124881 + GSM2802167_r1 + + + + + + SRS2561261 + SAMN07730383 + GSM2802167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237533 + + GSM2802166: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561260 + GSM2802166 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802166 + + + + + + + GEO Accession + GSM2802166 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561260 + SAMN07730384 + GSM2802166 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561260 + SAMN07730384 + GSM2802166 + + + + + + + SRR6124880 + GSM2802166_r1 + + + + + + SRS2561260 + SAMN07730384 + GSM2802166 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237532 + + GSM2802165: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561258 + GSM2802165 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802165 + + + + + + + GEO Accession + GSM2802165 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561258 + SAMN07730385 + GSM2802165 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561258 + SAMN07730385 + GSM2802165 + + + + + + + SRR6124879 + GSM2802165_r1 + + + + + + SRS2561258 + SAMN07730385 + GSM2802165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237531 + + GSM2802164: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561259 + GSM2802164 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802164 + + + + + + + GEO Accession + GSM2802164 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561259 + SAMN07730386 + GSM2802164 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561259 + SAMN07730386 + GSM2802164 + + + + + + + SRR6124878 + GSM2802164_r1 + + + + + + SRS2561259 + SAMN07730386 + GSM2802164 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237530 + + GSM2802163: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561257 + GSM2802163 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802163 + + + + + + + GEO Accession + GSM2802163 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561257 + SAMN07730387 + GSM2802163 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561257 + SAMN07730387 + GSM2802163 + + + + + + + SRR6124877 + GSM2802163_r1 + + + + + + SRS2561257 + SAMN07730387 + GSM2802163 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237529 + + GSM2802162: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561256 + GSM2802162 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802162 + + + + + + + GEO Accession + GSM2802162 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561256 + SAMN07730388 + GSM2802162 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561256 + SAMN07730388 + GSM2802162 + + + + + + + SRR6124876 + GSM2802162_r1 + + + + + + SRS2561256 + SAMN07730388 + GSM2802162 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237528 + + GSM2802161: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561254 + GSM2802161 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802161 + + + + + + + GEO Accession + GSM2802161 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561254 + SAMN07730389 + GSM2802161 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561254 + SAMN07730389 + GSM2802161 + + + + + + + SRR6124875 + GSM2802161_r1 + + + + + + SRS2561254 + SAMN07730389 + GSM2802161 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237527 + + GSM2802160: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561255 + GSM2802160 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802160 + + + + + + + GEO Accession + GSM2802160 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561255 + SAMN07730390 + GSM2802160 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561255 + SAMN07730390 + GSM2802160 + + + + + + + SRR6124874 + GSM2802160_r1 + + + + + + SRS2561255 + SAMN07730390 + GSM2802160 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237526 + + GSM2802159: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561252 + GSM2802159 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802159 + + + + + + + GEO Accession + GSM2802159 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561252 + SAMN07730391 + GSM2802159 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561252 + SAMN07730391 + GSM2802159 + + + + + + + SRR6124873 + GSM2802159_r1 + + + + + + SRS2561252 + SAMN07730391 + GSM2802159 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237525 + + GSM2802158: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561253 + GSM2802158 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802158 + + + + + + + GEO Accession + GSM2802158 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561253 + SAMN07730392 + GSM2802158 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561253 + SAMN07730392 + GSM2802158 + + + + + + + SRR6124872 + GSM2802158_r1 + + + + + + SRS2561253 + SAMN07730392 + GSM2802158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237524 + + GSM2802157: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561251 + GSM2802157 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802157 + + + + + + + GEO Accession + GSM2802157 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561251 + SAMN07730393 + GSM2802157 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561251 + SAMN07730393 + GSM2802157 + + + + + + + SRR6124871 + GSM2802157_r1 + + + + + + SRS2561251 + SAMN07730393 + GSM2802157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237523 + + GSM2802156: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561248 + GSM2802156 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802156 + + + + + + + GEO Accession + GSM2802156 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561248 + SAMN07730394 + GSM2802156 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561248 + SAMN07730394 + GSM2802156 + + + + + + + SRR6124870 + GSM2802156_r1 + + + + + + SRS2561248 + SAMN07730394 + GSM2802156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237522 + + GSM2802155: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561250 + GSM2802155 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802155 + + + + + + + GEO Accession + GSM2802155 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561250 + SAMN07730397 + GSM2802155 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561250 + SAMN07730397 + GSM2802155 + + + + + + + SRR6124869 + GSM2802155_r1 + + + + + + SRS2561250 + SAMN07730397 + GSM2802155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237521 + + GSM2802154: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561249 + GSM2802154 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802154 + + + + + + + GEO Accession + GSM2802154 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561249 + SAMN07730398 + GSM2802154 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561249 + SAMN07730398 + GSM2802154 + + + + + + + SRR6124868 + GSM2802154_r1 + + + + + + SRS2561249 + SAMN07730398 + GSM2802154 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237520 + + GSM2802153: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561247 + GSM2802153 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802153 + + + + + + + GEO Accession + GSM2802153 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561247 + SAMN07730399 + GSM2802153 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561247 + SAMN07730399 + GSM2802153 + + + + + + + SRR6124867 + GSM2802153_r1 + + + + + + SRS2561247 + SAMN07730399 + GSM2802153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237519 + + GSM2802152: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561246 + GSM2802152 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802152 + + + + + + + GEO Accession + GSM2802152 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561246 + SAMN07730400 + GSM2802152 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561246 + SAMN07730400 + GSM2802152 + + + + + + + SRR6124866 + GSM2802152_r1 + + + + + + SRS2561246 + SAMN07730400 + GSM2802152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237518 + + GSM2802151: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561245 + GSM2802151 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802151 + + + + + + + GEO Accession + GSM2802151 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561245 + SAMN07730395 + GSM2802151 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561245 + SAMN07730395 + GSM2802151 + + + + + + + SRR6124865 + GSM2802151_r1 + + + + + + SRS2561245 + SAMN07730395 + GSM2802151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237517 + + GSM2802150: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561244 + GSM2802150 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802150 + + + + + + + GEO Accession + GSM2802150 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561244 + SAMN07730396 + GSM2802150 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561244 + SAMN07730396 + GSM2802150 + + + + + + + SRR6124864 + GSM2802150_r1 + + + + + + SRS2561244 + SAMN07730396 + GSM2802150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237516 + + GSM2802149: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561243 + GSM2802149 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802149 + + + + + + + GEO Accession + GSM2802149 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561243 + SAMN07730401 + GSM2802149 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561243 + SAMN07730401 + GSM2802149 + + + + + + + SRR6124863 + GSM2802149_r1 + + + + + + SRS2561243 + SAMN07730401 + GSM2802149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237515 + + GSM2802148: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561242 + GSM2802148 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802148 + + + + + + + GEO Accession + GSM2802148 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561242 + SAMN07730402 + GSM2802148 + + U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561242 + SAMN07730402 + GSM2802148 + + + + + + + SRR6124862 + GSM2802148_r1 + + + + + + SRS2561242 + SAMN07730402 + GSM2802148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237514 + + GSM2802147: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561238 + GSM2802147 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802147 + + + + + + + GEO Accession + GSM2802147 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561238 + SAMN07730403 + GSM2802147 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561238 + SAMN07730403 + GSM2802147 + + + + + + + SRR6124861 + GSM2802147_r1 + + + + + + SRS2561238 + SAMN07730403 + GSM2802147 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237513 + + GSM2802146: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561239 + GSM2802146 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802146 + + + + + + + GEO Accession + GSM2802146 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561239 + SAMN07730688 + GSM2802146 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561239 + SAMN07730688 + GSM2802146 + + + + + + + SRR6124860 + GSM2802146_r1 + + + + + + SRS2561239 + SAMN07730688 + GSM2802146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237512 + + GSM2802145: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561240 + GSM2802145 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802145 + + + + + + + GEO Accession + GSM2802145 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561240 + SAMN07730689 + GSM2802145 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561240 + SAMN07730689 + GSM2802145 + + + + + + + SRR6124859 + GSM2802145_r1 + + + + + + SRS2561240 + SAMN07730689 + GSM2802145 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237511 + + GSM2802144: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561237 + GSM2802144 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802144 + + + + + + + GEO Accession + GSM2802144 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561237 + SAMN07730690 + GSM2802144 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561237 + SAMN07730690 + GSM2802144 + + + + + + + SRR6124858 + GSM2802144_r1 + + + + + + SRS2561237 + SAMN07730690 + GSM2802144 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237510 + + GSM2802143: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561235 + GSM2802143 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802143 + + + + + + + GEO Accession + GSM2802143 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561235 + SAMN07730691 + GSM2802143 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561235 + SAMN07730691 + GSM2802143 + + + + + + + SRR6124857 + GSM2802143_r1 + + + + + + SRS2561235 + SAMN07730691 + GSM2802143 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237509 + + GSM2802142: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561236 + GSM2802142 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802142 + + + + + + + GEO Accession + GSM2802142 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561236 + SAMN07730692 + GSM2802142 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561236 + SAMN07730692 + GSM2802142 + + + + + + + SRR6124856 + GSM2802142_r1 + + + + + + SRS2561236 + SAMN07730692 + GSM2802142 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237508 + + GSM2802141: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561234 + GSM2802141 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802141 + + + + + + + GEO Accession + GSM2802141 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561234 + SAMN07730693 + GSM2802141 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561234 + SAMN07730693 + GSM2802141 + + + + + + + SRR6124855 + GSM2802141_r1 + + + + + + SRS2561234 + SAMN07730693 + GSM2802141 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237507 + + GSM2802140: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561233 + GSM2802140 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802140 + + + + + + + GEO Accession + GSM2802140 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561233 + SAMN07730694 + GSM2802140 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561233 + SAMN07730694 + GSM2802140 + + + + + + + SRR6124854 + GSM2802140_r1 + + + + + + SRS2561233 + SAMN07730694 + GSM2802140 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237506 + + GSM2802139: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561232 + GSM2802139 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802139 + + + + + + + GEO Accession + GSM2802139 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561232 + SAMN07730695 + GSM2802139 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561232 + SAMN07730695 + GSM2802139 + + + + + + + SRR6124853 + GSM2802139_r1 + + + + + + SRS2561232 + SAMN07730695 + GSM2802139 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237505 + + GSM2802138: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561231 + GSM2802138 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802138 + + + + + + + GEO Accession + GSM2802138 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561231 + SAMN07730696 + GSM2802138 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561231 + SAMN07730696 + GSM2802138 + + + + + + + SRR6124852 + GSM2802138_r1 + + + + + + SRS2561231 + SAMN07730696 + GSM2802138 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237504 + + GSM2802137: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561230 + GSM2802137 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802137 + + + + + + + GEO Accession + GSM2802137 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561230 + SAMN07730697 + GSM2802137 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561230 + SAMN07730697 + GSM2802137 + + + + + + + SRR6124851 + GSM2802137_r1 + + + + + + SRS2561230 + SAMN07730697 + GSM2802137 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237503 + + GSM2802136: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561229 + GSM2802136 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802136 + + + + + + + GEO Accession + GSM2802136 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561229 + SAMN07730698 + GSM2802136 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561229 + SAMN07730698 + GSM2802136 + + + + + + + SRR6124850 + GSM2802136_r1 + + + + + + SRS2561229 + SAMN07730698 + GSM2802136 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237502 + + GSM2802135: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561228 + GSM2802135 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802135 + + + + + + + GEO Accession + GSM2802135 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561228 + SAMN07730699 + GSM2802135 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561228 + SAMN07730699 + GSM2802135 + + + + + + + SRR6124849 + GSM2802135_r1 + + + + + + SRS2561228 + SAMN07730699 + GSM2802135 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237501 + + GSM2802134: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561227 + GSM2802134 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802134 + + + + + + + GEO Accession + GSM2802134 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561227 + SAMN07730700 + GSM2802134 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561227 + SAMN07730700 + GSM2802134 + + + + + + + SRR6124848 + GSM2802134_r1 + + + + + + SRS2561227 + SAMN07730700 + GSM2802134 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237500 + + GSM2802133: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561226 + GSM2802133 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802133 + + + + + + + GEO Accession + GSM2802133 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561226 + SAMN07730701 + GSM2802133 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561226 + SAMN07730701 + GSM2802133 + + + + + + + SRR6124847 + GSM2802133_r1 + + + + + + SRS2561226 + SAMN07730701 + GSM2802133 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237499 + + GSM2802132: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561223 + GSM2802132 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802132 + + + + + + + GEO Accession + GSM2802132 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561223 + SAMN07730702 + GSM2802132 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561223 + SAMN07730702 + GSM2802132 + + + + + + + SRR6124846 + GSM2802132_r1 + + + + + + SRS2561223 + SAMN07730702 + GSM2802132 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237498 + + GSM2802131: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561225 + GSM2802131 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802131 + + + + + + + GEO Accession + GSM2802131 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561225 + SAMN07730216 + GSM2802131 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561225 + SAMN07730216 + GSM2802131 + + + + + + + SRR6124845 + GSM2802131_r1 + + + + + + SRS2561225 + SAMN07730216 + GSM2802131 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237497 + + GSM2802130: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561224 + GSM2802130 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802130 + + + + + + + GEO Accession + GSM2802130 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561224 + SAMN07730217 + GSM2802130 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561224 + SAMN07730217 + GSM2802130 + + + + + + + SRR6124844 + GSM2802130_r1 + + + + + + SRS2561224 + SAMN07730217 + GSM2802130 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237496 + + GSM2802129: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561222 + GSM2802129 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802129 + + + + + + + GEO Accession + GSM2802129 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561222 + SAMN07730218 + GSM2802129 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561222 + SAMN07730218 + GSM2802129 + + + + + + + SRR6124843 + GSM2802129_r1 + + + + + + SRS2561222 + SAMN07730218 + GSM2802129 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237495 + + GSM2802128: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561221 + GSM2802128 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802128 + + + + + + + GEO Accession + GSM2802128 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561221 + SAMN07730219 + GSM2802128 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561221 + SAMN07730219 + GSM2802128 + + + + + + + SRR6124842 + GSM2802128_r1 + + + + + + SRS2561221 + SAMN07730219 + GSM2802128 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237494 + + GSM2802127: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561220 + GSM2802127 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802127 + + + + + + + GEO Accession + GSM2802127 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561220 + SAMN07730220 + GSM2802127 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561220 + SAMN07730220 + GSM2802127 + + + + + + + SRR6124841 + GSM2802127_r1 + + + + + + SRS2561220 + SAMN07730220 + GSM2802127 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237493 + + GSM2802126: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561217 + GSM2802126 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802126 + + + + + + + GEO Accession + GSM2802126 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561217 + SAMN07730221 + GSM2802126 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561217 + SAMN07730221 + GSM2802126 + + + + + + + SRR6124840 + GSM2802126_r1 + + + + + + SRS2561217 + SAMN07730221 + GSM2802126 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237492 + + GSM2802125: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561218 + GSM2802125 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802125 + + + + + + + GEO Accession + GSM2802125 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561218 + SAMN07730222 + GSM2802125 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561218 + SAMN07730222 + GSM2802125 + + + + + + + SRR6124839 + GSM2802125_r1 + + + + + + SRS2561218 + SAMN07730222 + GSM2802125 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237491 + + GSM2802124: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561219 + GSM2802124 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802124 + + + + + + + GEO Accession + GSM2802124 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561219 + SAMN07730223 + GSM2802124 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561219 + SAMN07730223 + GSM2802124 + + + + + + + SRR6124838 + GSM2802124_r1 + + + + + + SRS2561219 + SAMN07730223 + GSM2802124 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237490 + + GSM2802123: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561216 + GSM2802123 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802123 + + + + + + + GEO Accession + GSM2802123 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561216 + SAMN07730227 + GSM2802123 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561216 + SAMN07730227 + GSM2802123 + + + + + + + SRR6124837 + GSM2802123_r1 + + + + + + SRS2561216 + SAMN07730227 + GSM2802123 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237489 + + GSM2802122: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561215 + GSM2802122 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802122 + + + + + + + GEO Accession + GSM2802122 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561215 + SAMN07730228 + GSM2802122 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561215 + SAMN07730228 + GSM2802122 + + + + + + + SRR6124836 + GSM2802122_r1 + + + + + + SRS2561215 + SAMN07730228 + GSM2802122 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237488 + + GSM2802121: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561214 + GSM2802121 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802121 + + + + + + + GEO Accession + GSM2802121 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561214 + SAMN07730224 + GSM2802121 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561214 + SAMN07730224 + GSM2802121 + + + + + + + SRR6124835 + GSM2802121_r1 + + + + + + SRS2561214 + SAMN07730224 + GSM2802121 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237487 + + GSM2802120: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561213 + GSM2802120 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802120 + + + + + + + GEO Accession + GSM2802120 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561213 + SAMN07730225 + GSM2802120 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561213 + SAMN07730225 + GSM2802120 + + + + + + + SRR6124834 + GSM2802120_r1 + + + + + + SRS2561213 + SAMN07730225 + GSM2802120 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237486 + + GSM2802119: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561212 + GSM2802119 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802119 + + + + + + + GEO Accession + GSM2802119 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561212 + SAMN07730226 + GSM2802119 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561212 + SAMN07730226 + GSM2802119 + + + + + + + SRR6124833 + GSM2802119_r1 + + + + + + SRS2561212 + SAMN07730226 + GSM2802119 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237485 + + GSM2802118: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561211 + GSM2802118 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802118 + + + + + + + GEO Accession + GSM2802118 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561211 + SAMN07730229 + GSM2802118 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561211 + SAMN07730229 + GSM2802118 + + + + + + + SRR6124832 + GSM2802118_r1 + + + + + + SRS2561211 + SAMN07730229 + GSM2802118 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237484 + + GSM2802117: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561210 + GSM2802117 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802117 + + + + + + + GEO Accession + GSM2802117 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561210 + SAMN07730230 + GSM2802117 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561210 + SAMN07730230 + GSM2802117 + + + + + + + SRR6124831 + GSM2802117_r1 + + + + + + SRS2561210 + SAMN07730230 + GSM2802117 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237483 + + GSM2802116: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561208 + GSM2802116 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802116 + + + + + + + GEO Accession + GSM2802116 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561208 + SAMN07730231 + GSM2802116 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561208 + SAMN07730231 + GSM2802116 + + + + + + + SRR6124830 + GSM2802116_r1 + + + + + + SRS2561208 + SAMN07730231 + GSM2802116 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237482 + + GSM2802115: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561209 + GSM2802115 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802115 + + + + + + + GEO Accession + GSM2802115 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561209 + SAMN07730232 + GSM2802115 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561209 + SAMN07730232 + GSM2802115 + + + + + + + SRR6124829 + GSM2802115_r1 + + + + + + SRS2561209 + SAMN07730232 + GSM2802115 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237481 + + GSM2802114: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561207 + GSM2802114 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802114 + + + + + + + GEO Accession + GSM2802114 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561207 + SAMN07730233 + GSM2802114 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561207 + SAMN07730233 + GSM2802114 + + + + + + + SRR6124828 + GSM2802114_r1 + + + + + + SRS2561207 + SAMN07730233 + GSM2802114 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237480 + + GSM2802113: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561206 + GSM2802113 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802113 + + + + + + + GEO Accession + GSM2802113 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561206 + SAMN07730234 + GSM2802113 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561206 + SAMN07730234 + GSM2802113 + + + + + + + SRR6124827 + GSM2802113_r1 + + + + + + SRS2561206 + SAMN07730234 + GSM2802113 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237479 + + GSM2802112: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561205 + GSM2802112 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802112 + + + + + + + GEO Accession + GSM2802112 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561205 + SAMN07730235 + GSM2802112 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561205 + SAMN07730235 + GSM2802112 + + + + + + + SRR6124826 + GSM2802112_r1 + + + + + + SRS2561205 + SAMN07730235 + GSM2802112 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237478 + + GSM2802111: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561203 + GSM2802111 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802111 + + + + + + + GEO Accession + GSM2802111 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561203 + SAMN07730236 + GSM2802111 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561203 + SAMN07730236 + GSM2802111 + + + + + + + SRR6124825 + GSM2802111_r1 + + + + + + SRS2561203 + SAMN07730236 + GSM2802111 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237477 + + GSM2802110: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561204 + GSM2802110 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802110 + + + + + + + GEO Accession + GSM2802110 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561204 + SAMN07730237 + GSM2802110 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561204 + SAMN07730237 + GSM2802110 + + + + + + + SRR6124824 + GSM2802110_r1 + + + + + + SRS2561204 + SAMN07730237 + GSM2802110 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237476 + + GSM2802109: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561202 + GSM2802109 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802109 + + + + + + + GEO Accession + GSM2802109 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561202 + SAMN07730238 + GSM2802109 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561202 + SAMN07730238 + GSM2802109 + + + + + + + SRR6124823 + GSM2802109_r1 + + + + + + SRS2561202 + SAMN07730238 + GSM2802109 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237475 + + GSM2802108: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561201 + GSM2802108 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802108 + + + + + + + GEO Accession + GSM2802108 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561201 + SAMN07730239 + GSM2802108 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561201 + SAMN07730239 + GSM2802108 + + + + + + + SRR6124822 + GSM2802108_r1 + + + + + + SRS2561201 + SAMN07730239 + GSM2802108 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237474 + + GSM2802107: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561200 + GSM2802107 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802107 + + + + + + + GEO Accession + GSM2802107 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561200 + SAMN07730240 + GSM2802107 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561200 + SAMN07730240 + GSM2802107 + + + + + + + SRR6124821 + GSM2802107_r1 + + + + + + SRS2561200 + SAMN07730240 + GSM2802107 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237473 + + GSM2802106: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561199 + GSM2802106 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802106 + + + + + + + GEO Accession + GSM2802106 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561199 + SAMN07730241 + GSM2802106 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561199 + SAMN07730241 + GSM2802106 + + + + + + + SRR6124820 + GSM2802106_r1 + + + + + + SRS2561199 + SAMN07730241 + GSM2802106 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237472 + + GSM2802105: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561198 + GSM2802105 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802105 + + + + + + + GEO Accession + GSM2802105 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561198 + SAMN07730242 + GSM2802105 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561198 + SAMN07730242 + GSM2802105 + + + + + + + SRR6124819 + GSM2802105_r1 + + + + + + SRS2561198 + SAMN07730242 + GSM2802105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237471 + + GSM2802104: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561197 + GSM2802104 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802104 + + + + + + + GEO Accession + GSM2802104 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561197 + SAMN07730470 + GSM2802104 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561197 + SAMN07730470 + GSM2802104 + + + + + + + SRR6124818 + GSM2802104_r1 + + + + + + SRS2561197 + SAMN07730470 + GSM2802104 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237470 + + GSM2802103: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561196 + GSM2802103 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802103 + + + + + + + GEO Accession + GSM2802103 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561196 + SAMN07730471 + GSM2802103 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561196 + SAMN07730471 + GSM2802103 + + + + + + + SRR6124817 + GSM2802103_r1 + + + + + + SRS2561196 + SAMN07730471 + GSM2802103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237469 + + GSM2802102: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561195 + GSM2802102 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802102 + + + + + + + GEO Accession + GSM2802102 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561195 + SAMN07730472 + GSM2802102 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561195 + SAMN07730472 + GSM2802102 + + + + + + + SRR6124816 + GSM2802102_r1 + + + + + + SRS2561195 + SAMN07730472 + GSM2802102 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237468 + + GSM2802101: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561194 + GSM2802101 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802101 + + + + + + + GEO Accession + GSM2802101 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561194 + SAMN07730473 + GSM2802101 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561194 + SAMN07730473 + GSM2802101 + + + + + + + SRR6124815 + GSM2802101_r1 + + + + + + SRS2561194 + SAMN07730473 + GSM2802101 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237467 + + GSM2802100: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561192 + GSM2802100 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802100 + + + + + + + GEO Accession + GSM2802100 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561192 + SAMN07730474 + GSM2802100 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561192 + SAMN07730474 + GSM2802100 + + + + + + + SRR6124814 + GSM2802100_r1 + + + + + + SRS2561192 + SAMN07730474 + GSM2802100 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237466 + + GSM2802099: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561191 + GSM2802099 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802099 + + + + + + + GEO Accession + GSM2802099 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561191 + SAMN07730475 + GSM2802099 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561191 + SAMN07730475 + GSM2802099 + + + + + + + SRR6124813 + GSM2802099_r1 + + + + + + SRS2561191 + SAMN07730475 + GSM2802099 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237465 + + GSM2802098: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561190 + GSM2802098 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802098 + + + + + + + GEO Accession + GSM2802098 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561190 + SAMN07730476 + GSM2802098 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561190 + SAMN07730476 + GSM2802098 + + + + + + + SRR6124812 + GSM2802098_r1 + + + + + + SRS2561190 + SAMN07730476 + GSM2802098 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237464 + + GSM2802097: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561189 + GSM2802097 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802097 + + + + + + + GEO Accession + GSM2802097 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561189 + SAMN07730477 + GSM2802097 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561189 + SAMN07730477 + GSM2802097 + + + + + + + SRR6124811 + GSM2802097_r1 + + + + + + SRS2561189 + SAMN07730477 + GSM2802097 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237463 + + GSM2802096: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561188 + GSM2802096 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802096 + + + + + + + GEO Accession + GSM2802096 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561188 + SAMN07730478 + GSM2802096 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561188 + SAMN07730478 + GSM2802096 + + + + + + + SRR6124810 + GSM2802096_r1 + + + + + + SRS2561188 + SAMN07730478 + GSM2802096 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237462 + + GSM2802095: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561187 + GSM2802095 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802095 + + + + + + + GEO Accession + GSM2802095 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561187 + SAMN07730479 + GSM2802095 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561187 + SAMN07730479 + GSM2802095 + + + + + + + SRR6124809 + GSM2802095_r1 + + + + + + SRS2561187 + SAMN07730479 + GSM2802095 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237461 + + GSM2802094: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561186 + GSM2802094 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802094 + + + + + + + GEO Accession + GSM2802094 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561186 + SAMN07730480 + GSM2802094 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561186 + SAMN07730480 + GSM2802094 + + + + + + + SRR6124808 + GSM2802094_r1 + + + + + + SRS2561186 + SAMN07730480 + GSM2802094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237460 + + GSM2802093: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561185 + GSM2802093 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802093 + + + + + + + GEO Accession + GSM2802093 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561185 + SAMN07730481 + GSM2802093 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561185 + SAMN07730481 + GSM2802093 + + + + + + + SRR6124807 + GSM2802093_r1 + + + + + + SRS2561185 + SAMN07730481 + GSM2802093 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237459 + + GSM2802092: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561184 + GSM2802092 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802092 + + + + + + + GEO Accession + GSM2802092 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561184 + SAMN07730482 + GSM2802092 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561184 + SAMN07730482 + GSM2802092 + + + + + + + SRR6124806 + GSM2802092_r1 + + + + + + SRS2561184 + SAMN07730482 + GSM2802092 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237458 + + GSM2802091: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561183 + GSM2802091 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802091 + + + + + + + GEO Accession + GSM2802091 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561183 + SAMN07730483 + GSM2802091 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561183 + SAMN07730483 + GSM2802091 + + + + + + + SRR6124805 + GSM2802091_r1 + + + + + + SRS2561183 + SAMN07730483 + GSM2802091 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237457 + + GSM2802090: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561182 + GSM2802090 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802090 + + + + + + + GEO Accession + GSM2802090 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561182 + SAMN07730484 + GSM2802090 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561182 + SAMN07730484 + GSM2802090 + + + + + + + SRR6124804 + GSM2802090_r1 + + + + + + SRS2561182 + SAMN07730484 + GSM2802090 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237456 + + GSM2802089: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561181 + GSM2802089 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802089 + + + + + + + GEO Accession + GSM2802089 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561181 + SAMN07730485 + GSM2802089 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561181 + SAMN07730485 + GSM2802089 + + + + + + + SRR6124803 + GSM2802089_r1 + + + + + + SRS2561181 + SAMN07730485 + GSM2802089 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237455 + + GSM2802088: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561180 + GSM2802088 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802088 + + + + + + + GEO Accession + GSM2802088 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561180 + SAMN07730486 + GSM2802088 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561180 + SAMN07730486 + GSM2802088 + + + + + + + SRR6124802 + GSM2802088_r1 + + + + + + SRS2561180 + SAMN07730486 + GSM2802088 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237454 + + GSM2802087: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561179 + GSM2802087 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802087 + + + + + + + GEO Accession + GSM2802087 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561179 + SAMN07730487 + GSM2802087 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561179 + SAMN07730487 + GSM2802087 + + + + + + + SRR6124801 + GSM2802087_r1 + + + + + + SRS2561179 + SAMN07730487 + GSM2802087 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237453 + + GSM2802086: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561178 + GSM2802086 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802086 + + + + + + + GEO Accession + GSM2802086 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561178 + SAMN07730488 + GSM2802086 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561178 + SAMN07730488 + GSM2802086 + + + + + + + SRR6124800 + GSM2802086_r1 + + + + + + SRS2561178 + SAMN07730488 + GSM2802086 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237452 + + GSM2802085: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561177 + GSM2802085 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802085 + + + + + + + GEO Accession + GSM2802085 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561177 + SAMN07730489 + GSM2802085 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561177 + SAMN07730489 + GSM2802085 + + + + + + + SRR6124799 + GSM2802085_r1 + + + + + + SRS2561177 + SAMN07730489 + GSM2802085 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237451 + + GSM2802084: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561176 + GSM2802084 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802084 + + + + + + + GEO Accession + GSM2802084 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561176 + SAMN07730490 + GSM2802084 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561176 + SAMN07730490 + GSM2802084 + + + + + + + SRR6124798 + GSM2802084_r1 + + + + + + SRS2561176 + SAMN07730490 + GSM2802084 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237450 + + GSM2802083: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561175 + GSM2802083 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802083 + + + + + + + GEO Accession + GSM2802083 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561175 + SAMN07730491 + GSM2802083 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561175 + SAMN07730491 + GSM2802083 + + + + + + + SRR6124797 + GSM2802083_r1 + + + + + + SRS2561175 + SAMN07730491 + GSM2802083 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237449 + + GSM2802082: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561174 + GSM2802082 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802082 + + + + + + + GEO Accession + GSM2802082 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561174 + SAMN07730492 + GSM2802082 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561174 + SAMN07730492 + GSM2802082 + + + + + + + SRR6124796 + GSM2802082_r1 + + + + + + SRS2561174 + SAMN07730492 + GSM2802082 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237448 + + GSM2802081: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561173 + GSM2802081 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802081 + + + + + + + GEO Accession + GSM2802081 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561173 + SAMN07730493 + GSM2802081 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561173 + SAMN07730493 + GSM2802081 + + + + + + + SRR6124795 + GSM2802081_r1 + + + + + + SRS2561173 + SAMN07730493 + GSM2802081 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237447 + + GSM2802080: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561172 + GSM2802080 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802080 + + + + + + + GEO Accession + GSM2802080 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561172 + SAMN07730494 + GSM2802080 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561172 + SAMN07730494 + GSM2802080 + + + + + + + SRR6124794 + GSM2802080_r1 + + + + + + SRS2561172 + SAMN07730494 + GSM2802080 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237446 + + GSM2802079: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561171 + GSM2802079 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802079 + + + + + + + GEO Accession + GSM2802079 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561171 + SAMN07730495 + GSM2802079 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561171 + SAMN07730495 + GSM2802079 + + + + + + + SRR6124793 + GSM2802079_r1 + + + + + + SRS2561171 + SAMN07730495 + GSM2802079 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237445 + + GSM2802078: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561170 + GSM2802078 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802078 + + + + + + + GEO Accession + GSM2802078 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561170 + SAMN07730496 + GSM2802078 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561170 + SAMN07730496 + GSM2802078 + + + + + + + SRR6124792 + GSM2802078_r1 + + + + + + SRS2561170 + SAMN07730496 + GSM2802078 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237444 + + GSM2802077: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561169 + GSM2802077 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802077 + + + + + + + GEO Accession + GSM2802077 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561169 + SAMN07730497 + GSM2802077 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561169 + SAMN07730497 + GSM2802077 + + + + + + + SRR6124791 + GSM2802077_r1 + + + + + + SRS2561169 + SAMN07730497 + GSM2802077 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237443 + + GSM2802076: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561168 + GSM2802076 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802076 + + + + + + + GEO Accession + GSM2802076 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561168 + SAMN07730498 + GSM2802076 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561168 + SAMN07730498 + GSM2802076 + + + + + + + SRR6124790 + GSM2802076_r1 + + + + + + SRS2561168 + SAMN07730498 + GSM2802076 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237442 + + GSM2802075: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561167 + GSM2802075 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802075 + + + + + + + GEO Accession + GSM2802075 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561167 + SAMN07730499 + GSM2802075 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561167 + SAMN07730499 + GSM2802075 + + + + + + + SRR6124789 + GSM2802075_r1 + + + + + + SRS2561167 + SAMN07730499 + GSM2802075 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237441 + + GSM2802074: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561166 + GSM2802074 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802074 + + + + + + + GEO Accession + GSM2802074 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561166 + SAMN07730293 + GSM2802074 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561166 + SAMN07730293 + GSM2802074 + + + + + + + SRR6124788 + GSM2802074_r1 + + + + + + SRS2561166 + SAMN07730293 + GSM2802074 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237440 + + GSM2802073: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561165 + GSM2802073 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802073 + + + + + + + GEO Accession + GSM2802073 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561165 + SAMN07730294 + GSM2802073 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561165 + SAMN07730294 + GSM2802073 + + + + + + + SRR6124787 + GSM2802073_r1 + + + + + + SRS2561165 + SAMN07730294 + GSM2802073 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237439 + + GSM2802072: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561164 + GSM2802072 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802072 + + + + + + + GEO Accession + GSM2802072 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561164 + SAMN07730295 + GSM2802072 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561164 + SAMN07730295 + GSM2802072 + + + + + + + SRR6124786 + GSM2802072_r1 + + + + + + SRS2561164 + SAMN07730295 + GSM2802072 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237438 + + GSM2802071: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561241 + GSM2802071 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802071 + + + + + + + GEO Accession + GSM2802071 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561241 + SAMN07730296 + GSM2802071 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561241 + SAMN07730296 + GSM2802071 + + + + + + + SRR6124785 + GSM2802071_r1 + + + + + + SRS2561241 + SAMN07730296 + GSM2802071 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237437 + + GSM2802070: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561163 + GSM2802070 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802070 + + + + + + + GEO Accession + GSM2802070 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561163 + SAMN07730297 + GSM2802070 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561163 + SAMN07730297 + GSM2802070 + + + + + + + SRR6124784 + GSM2802070_r1 + + + + + + SRS2561163 + SAMN07730297 + GSM2802070 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237436 + + GSM2802069: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561161 + GSM2802069 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802069 + + + + + + + GEO Accession + GSM2802069 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561161 + SAMN07730298 + GSM2802069 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561161 + SAMN07730298 + GSM2802069 + + + + + + + SRR6124783 + GSM2802069_r1 + + + + + + SRS2561161 + SAMN07730298 + GSM2802069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237435 + + GSM2802068: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561162 + GSM2802068 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802068 + + + + + + + GEO Accession + GSM2802068 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561162 + SAMN07730299 + GSM2802068 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561162 + SAMN07730299 + GSM2802068 + + + + + + + SRR6124782 + GSM2802068_r1 + + + + + + SRS2561162 + SAMN07730299 + GSM2802068 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237434 + + GSM2802067: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561160 + GSM2802067 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802067 + + + + + + + GEO Accession + GSM2802067 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561160 + SAMN07730300 + GSM2802067 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561160 + SAMN07730300 + GSM2802067 + + + + + + + SRR6124781 + GSM2802067_r1 + + + + + + SRS2561160 + SAMN07730300 + GSM2802067 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237433 + + GSM2802066: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561159 + GSM2802066 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802066 + + + + + + + GEO Accession + GSM2802066 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561159 + SAMN07730301 + GSM2802066 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561159 + SAMN07730301 + GSM2802066 + + + + + + + SRR6124780 + GSM2802066_r1 + + + + + + SRS2561159 + SAMN07730301 + GSM2802066 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237432 + + GSM2802065: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561158 + GSM2802065 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802065 + + + + + + + GEO Accession + GSM2802065 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561158 + SAMN07730302 + GSM2802065 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561158 + SAMN07730302 + GSM2802065 + + + + + + + SRR6124779 + GSM2802065_r1 + + + + + + SRS2561158 + SAMN07730302 + GSM2802065 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237431 + + GSM2802064: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561157 + GSM2802064 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802064 + + + + + + + GEO Accession + GSM2802064 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561157 + SAMN07730303 + GSM2802064 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561157 + SAMN07730303 + GSM2802064 + + + + + + + SRR6124778 + GSM2802064_r1 + + + + + + SRS2561157 + SAMN07730303 + GSM2802064 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237430 + + GSM2802063: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561156 + GSM2802063 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802063 + + + + + + + GEO Accession + GSM2802063 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561156 + SAMN07730304 + GSM2802063 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561156 + SAMN07730304 + GSM2802063 + + + + + + + SRR6124777 + GSM2802063_r1 + + + + + + SRS2561156 + SAMN07730304 + GSM2802063 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237429 + + GSM2802062: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561154 + GSM2802062 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802062 + + + + + + + GEO Accession + GSM2802062 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561154 + SAMN07730305 + GSM2802062 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561154 + SAMN07730305 + GSM2802062 + + + + + + + SRR6124776 + GSM2802062_r1 + + + + + + SRS2561154 + SAMN07730305 + GSM2802062 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237428 + + GSM2802061: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561155 + GSM2802061 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802061 + + + + + + + GEO Accession + GSM2802061 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561155 + SAMN07730306 + GSM2802061 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561155 + SAMN07730306 + GSM2802061 + + + + + + + SRR6124775 + GSM2802061_r1 + + + + + + SRS2561155 + SAMN07730306 + GSM2802061 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237427 + + GSM2802060: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561153 + GSM2802060 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802060 + + + + + + + GEO Accession + GSM2802060 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561153 + SAMN07730307 + GSM2802060 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561153 + SAMN07730307 + GSM2802060 + + + + + + + SRR6124774 + GSM2802060_r1 + + + + + + SRS2561153 + SAMN07730307 + GSM2802060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237426 + + GSM2802059: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561152 + GSM2802059 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802059 + + + + + + + GEO Accession + GSM2802059 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561152 + SAMN07730308 + GSM2802059 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561152 + SAMN07730308 + GSM2802059 + + + + + + + SRR6124773 + GSM2802059_r1 + + + + + + SRS2561152 + SAMN07730308 + GSM2802059 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237425 + + GSM2802058: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561151 + GSM2802058 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802058 + + + + + + + GEO Accession + GSM2802058 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561151 + SAMN07730309 + GSM2802058 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561151 + SAMN07730309 + GSM2802058 + + + + + + + SRR6124772 + GSM2802058_r1 + + + + + + SRS2561151 + SAMN07730309 + GSM2802058 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237424 + + GSM2802057: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561149 + GSM2802057 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802057 + + + + + + + GEO Accession + GSM2802057 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561149 + SAMN07730310 + GSM2802057 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561149 + SAMN07730310 + GSM2802057 + + + + + + + SRR6124771 + GSM2802057_r1 + + + + + + SRS2561149 + SAMN07730310 + GSM2802057 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237423 + + GSM2802056: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561148 + GSM2802056 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802056 + + + + + + + GEO Accession + GSM2802056 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561148 + SAMN07730311 + GSM2802056 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561148 + SAMN07730311 + GSM2802056 + + + + + + + SRR6124770 + GSM2802056_r1 + + + + + + SRS2561148 + SAMN07730311 + GSM2802056 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237422 + + GSM2802055: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561147 + GSM2802055 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802055 + + + + + + + GEO Accession + GSM2802055 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561147 + SAMN07730312 + GSM2802055 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561147 + SAMN07730312 + GSM2802055 + + + + + + + SRR6124769 + GSM2802055_r1 + + + + + + SRS2561147 + SAMN07730312 + GSM2802055 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237421 + + GSM2802054: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561146 + GSM2802054 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802054 + + + + + + + GEO Accession + GSM2802054 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561146 + SAMN07730313 + GSM2802054 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561146 + SAMN07730313 + GSM2802054 + + + + + + + SRR6124768 + GSM2802054_r1 + + + + + + SRS2561146 + SAMN07730313 + GSM2802054 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237420 + + GSM2802053: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561145 + GSM2802053 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802053 + + + + + + + GEO Accession + GSM2802053 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561145 + SAMN07730314 + GSM2802053 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561145 + SAMN07730314 + GSM2802053 + + + + + + + SRR6124767 + GSM2802053_r1 + + + + + + SRS2561145 + SAMN07730314 + GSM2802053 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237419 + + GSM2802052: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561144 + GSM2802052 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802052 + + + + + + + GEO Accession + GSM2802052 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561144 + SAMN07730315 + GSM2802052 + + U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561144 + SAMN07730315 + GSM2802052 + + + + + + + SRR6124766 + GSM2802052_r1 + + + + + + SRS2561144 + SAMN07730315 + GSM2802052 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237418 + + GSM2802051: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561143 + GSM2802051 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802051 + + + + + + + GEO Accession + GSM2802051 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561143 + SAMN07730316 + GSM2802051 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561143 + SAMN07730316 + GSM2802051 + + + + + + + SRR6124765 + GSM2802051_r1 + + + + + + SRS2561143 + SAMN07730316 + GSM2802051 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237417 + + GSM2802050: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561141 + GSM2802050 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802050 + + + + + + + GEO Accession + GSM2802050 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561141 + SAMN07730317 + GSM2802050 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561141 + SAMN07730317 + GSM2802050 + + + + + + + SRR6124764 + GSM2802050_r1 + + + + + + SRS2561141 + SAMN07730317 + GSM2802050 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237416 + + GSM2802049: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561142 + GSM2802049 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802049 + + + + + + + GEO Accession + GSM2802049 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561142 + SAMN07730318 + GSM2802049 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561142 + SAMN07730318 + GSM2802049 + + + + + + + SRR6124763 + GSM2802049_r1 + + + + + + SRS2561142 + SAMN07730318 + GSM2802049 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237415 + + GSM2802048: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561140 + GSM2802048 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802048 + + + + + + + GEO Accession + GSM2802048 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561140 + SAMN07730319 + GSM2802048 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561140 + SAMN07730319 + GSM2802048 + + + + + + + SRR6124762 + GSM2802048_r1 + + + + + + SRS2561140 + SAMN07730319 + GSM2802048 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237414 + + GSM2802047: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561139 + GSM2802047 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802047 + + + + + + + GEO Accession + GSM2802047 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561139 + SAMN07730320 + GSM2802047 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561139 + SAMN07730320 + GSM2802047 + + + + + + + SRR6124761 + GSM2802047_r1 + + + + + + SRS2561139 + SAMN07730320 + GSM2802047 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237413 + + GSM2802046: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561138 + GSM2802046 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802046 + + + + + + + GEO Accession + GSM2802046 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561138 + SAMN07730321 + GSM2802046 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561138 + SAMN07730321 + GSM2802046 + + + + + + + SRR6124760 + GSM2802046_r1 + + + + + + SRS2561138 + SAMN07730321 + GSM2802046 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237412 + + GSM2802045: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561137 + GSM2802045 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802045 + + + + + + + GEO Accession + GSM2802045 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561137 + SAMN07730322 + GSM2802045 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561137 + SAMN07730322 + GSM2802045 + + + + + + + SRR6124759 + GSM2802045_r1 + + + + + + SRS2561137 + SAMN07730322 + GSM2802045 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237411 + + GSM2802044: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561136 + GSM2802044 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802044 + + + + + + + GEO Accession + GSM2802044 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561136 + SAMN07730323 + GSM2802044 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561136 + SAMN07730323 + GSM2802044 + + + + + + + SRR6124758 + GSM2802044_r1 + + + + + + SRS2561136 + SAMN07730323 + GSM2802044 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237410 + + GSM2802043: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561135 + GSM2802043 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802043 + + + + + + + GEO Accession + GSM2802043 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561135 + SAMN07730324 + GSM2802043 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561135 + SAMN07730324 + GSM2802043 + + + + + + + SRR6124757 + GSM2802043_r1 + + + + + + SRS2561135 + SAMN07730324 + GSM2802043 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237409 + + GSM2802042: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561134 + GSM2802042 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802042 + + + + + + + GEO Accession + GSM2802042 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561134 + SAMN07730325 + GSM2802042 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561134 + SAMN07730325 + GSM2802042 + + + + + + + SRR6124756 + GSM2802042_r1 + + + + + + SRS2561134 + SAMN07730325 + GSM2802042 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237408 + + GSM2802041: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561133 + GSM2802041 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802041 + + + + + + + GEO Accession + GSM2802041 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561133 + SAMN07730326 + GSM2802041 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561133 + SAMN07730326 + GSM2802041 + + + + + + + SRR6124755 + GSM2802041_r1 + + + + + + SRS2561133 + SAMN07730326 + GSM2802041 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237407 + + GSM2802040: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561132 + GSM2802040 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802040 + + + + + + + GEO Accession + GSM2802040 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561132 + SAMN07730327 + GSM2802040 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561132 + SAMN07730327 + GSM2802040 + + + + + + + SRR6124754 + GSM2802040_r1 + + + + + + SRS2561132 + SAMN07730327 + GSM2802040 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237406 + + GSM2802039: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561131 + GSM2802039 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802039 + + + + + + + GEO Accession + GSM2802039 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561131 + SAMN07730328 + GSM2802039 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561131 + SAMN07730328 + GSM2802039 + + + + + + + SRR6124753 + GSM2802039_r1 + + + + + + SRS2561131 + SAMN07730328 + GSM2802039 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237405 + + GSM2802038: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561129 + GSM2802038 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802038 + + + + + + + GEO Accession + GSM2802038 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561129 + SAMN07730329 + GSM2802038 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561129 + SAMN07730329 + GSM2802038 + + + + + + + SRR6124752 + GSM2802038_r1 + + + + + + SRS2561129 + SAMN07730329 + GSM2802038 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237404 + + GSM2802037: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561130 + GSM2802037 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802037 + + + + + + + GEO Accession + GSM2802037 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561130 + SAMN07730330 + GSM2802037 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561130 + SAMN07730330 + GSM2802037 + + + + + + + SRR6124751 + GSM2802037_r1 + + + + + + SRS2561130 + SAMN07730330 + GSM2802037 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237403 + + GSM2802036: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561128 + GSM2802036 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802036 + + + + + + + GEO Accession + GSM2802036 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561128 + SAMN07730331 + GSM2802036 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561128 + SAMN07730331 + GSM2802036 + + + + + + + SRR6124750 + GSM2802036_r1 + + + + + + SRS2561128 + SAMN07730331 + GSM2802036 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237402 + + GSM2802035: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561127 + GSM2802035 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802035 + + + + + + + GEO Accession + GSM2802035 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561127 + SAMN07730332 + GSM2802035 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561127 + SAMN07730332 + GSM2802035 + + + + + + + SRR6124749 + GSM2802035_r1 + + + + + + SRS2561127 + SAMN07730332 + GSM2802035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237401 + + GSM2802034: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561126 + GSM2802034 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802034 + + + + + + + GEO Accession + GSM2802034 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561126 + SAMN07730333 + GSM2802034 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561126 + SAMN07730333 + GSM2802034 + + + + + + + SRR6124748 + GSM2802034_r1 + + + + + + SRS2561126 + SAMN07730333 + GSM2802034 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237400 + + GSM2802033: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561125 + GSM2802033 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802033 + + + + + + + GEO Accession + GSM2802033 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561125 + SAMN07730336 + GSM2802033 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561125 + SAMN07730336 + GSM2802033 + + + + + + + SRR6124747 + GSM2802033_r1 + + + + + + SRS2561125 + SAMN07730336 + GSM2802033 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237399 + + GSM2802032: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561124 + GSM2802032 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802032 + + + + + + + GEO Accession + GSM2802032 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561124 + SAMN07730337 + GSM2802032 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561124 + SAMN07730337 + GSM2802032 + + + + + + + SRR6124746 + GSM2802032_r1 + + + + + + SRS2561124 + SAMN07730337 + GSM2802032 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237398 + + GSM2802031: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561123 + GSM2802031 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802031 + + + + + + + GEO Accession + GSM2802031 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561123 + SAMN07730334 + GSM2802031 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561123 + SAMN07730334 + GSM2802031 + + + + + + + SRR6124745 + GSM2802031_r1 + + + + + + SRS2561123 + SAMN07730334 + GSM2802031 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237397 + + GSM2802030: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561122 + GSM2802030 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802030 + + + + + + + GEO Accession + GSM2802030 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561122 + SAMN07730335 + GSM2802030 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561122 + SAMN07730335 + GSM2802030 + + + + + + + SRR6124744 + GSM2802030_r1 + + + + + + SRS2561122 + SAMN07730335 + GSM2802030 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237396 + + GSM2802029: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561121 + GSM2802029 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802029 + + + + + + + GEO Accession + GSM2802029 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561121 + SAMN07730338 + GSM2802029 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561121 + SAMN07730338 + GSM2802029 + + + + + + + SRR6124743 + GSM2802029_r1 + + + + + + SRS2561121 + SAMN07730338 + GSM2802029 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237395 + + GSM2802028: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561120 + GSM2802028 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802028 + + + + + + + GEO Accession + GSM2802028 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561120 + SAMN07730339 + GSM2802028 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561120 + SAMN07730339 + GSM2802028 + + + + + + + SRR6124742 + GSM2802028_r1 + + + + + + SRS2561120 + SAMN07730339 + GSM2802028 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237394 + + GSM2802027: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561119 + GSM2802027 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802027 + + + + + + + GEO Accession + GSM2802027 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561119 + SAMN07730340 + GSM2802027 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561119 + SAMN07730340 + GSM2802027 + + + + + + + SRR6124741 + GSM2802027_r1 + + + + + + SRS2561119 + SAMN07730340 + GSM2802027 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237393 + + GSM2802026: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561118 + GSM2802026 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802026 + + + + + + + GEO Accession + GSM2802026 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561118 + SAMN07730341 + GSM2802026 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561118 + SAMN07730341 + GSM2802026 + + + + + + + SRR6124740 + GSM2802026_r1 + + + + + + SRS2561118 + SAMN07730341 + GSM2802026 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237392 + + GSM2802025: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561116 + GSM2802025 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802025 + + + + + + + GEO Accession + GSM2802025 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561116 + SAMN07730342 + GSM2802025 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561116 + SAMN07730342 + GSM2802025 + + + + + + + SRR6124739 + GSM2802025_r1 + + + + + + SRS2561116 + SAMN07730342 + GSM2802025 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237391 + + GSM2802024: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561117 + GSM2802024 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802024 + + + + + + + GEO Accession + GSM2802024 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561117 + SAMN07730343 + GSM2802024 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561117 + SAMN07730343 + GSM2802024 + + + + + + + SRR6124738 + GSM2802024_r1 + + + + + + SRS2561117 + SAMN07730343 + GSM2802024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237390 + + GSM2802023: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561115 + GSM2802023 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802023 + + + + + + + GEO Accession + GSM2802023 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561115 + SAMN07730344 + GSM2802023 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561115 + SAMN07730344 + GSM2802023 + + + + + + + SRR6124737 + GSM2802023_r1 + + + + + + SRS2561115 + SAMN07730344 + GSM2802023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237389 + + GSM2802022: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561113 + GSM2802022 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802022 + + + + + + + GEO Accession + GSM2802022 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561113 + SAMN07730345 + GSM2802022 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561113 + SAMN07730345 + GSM2802022 + + + + + + + SRR6124736 + GSM2802022_r1 + + + + + + SRS2561113 + SAMN07730345 + GSM2802022 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237388 + + GSM2802021: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561112 + GSM2802021 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802021 + + + + + + + GEO Accession + GSM2802021 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561112 + SAMN07730346 + GSM2802021 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561112 + SAMN07730346 + GSM2802021 + + + + + + + SRR6124735 + GSM2802021_r1 + + + + + + SRS2561112 + SAMN07730346 + GSM2802021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237387 + + GSM2802020: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561114 + GSM2802020 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802020 + + + + + + + GEO Accession + GSM2802020 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561114 + SAMN07730347 + GSM2802020 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561114 + SAMN07730347 + GSM2802020 + + + + + + + SRR6124734 + GSM2802020_r1 + + + + + + SRS2561114 + SAMN07730347 + GSM2802020 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237386 + + GSM2802019: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561111 + GSM2802019 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802019 + + + + + + + GEO Accession + GSM2802019 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561111 + SAMN07730348 + GSM2802019 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561111 + SAMN07730348 + GSM2802019 + + + + + + + SRR6124733 + GSM2802019_r1 + + + + + + SRS2561111 + SAMN07730348 + GSM2802019 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237385 + + GSM2802018: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561110 + GSM2802018 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802018 + + + + + + + GEO Accession + GSM2802018 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561110 + SAMN07730349 + GSM2802018 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561110 + SAMN07730349 + GSM2802018 + + + + + + + SRR6124732 + GSM2802018_r1 + + + + + + SRS2561110 + SAMN07730349 + GSM2802018 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237384 + + GSM2802017: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561109 + GSM2802017 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802017 + + + + + + + GEO Accession + GSM2802017 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561109 + SAMN07730350 + GSM2802017 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561109 + SAMN07730350 + GSM2802017 + + + + + + + SRR6124731 + GSM2802017_r1 + + + + + + SRS2561109 + SAMN07730350 + GSM2802017 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237383 + + GSM2802016: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561108 + GSM2802016 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802016 + + + + + + + GEO Accession + GSM2802016 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561108 + SAMN07730351 + GSM2802016 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561108 + SAMN07730351 + GSM2802016 + + + + + + + SRR6124730 + GSM2802016_r1 + + + + + + SRS2561108 + SAMN07730351 + GSM2802016 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237382 + + GSM2802015: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561107 + GSM2802015 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802015 + + + + + + + GEO Accession + GSM2802015 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561107 + SAMN07730352 + GSM2802015 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561107 + SAMN07730352 + GSM2802015 + + + + + + + SRR6124729 + GSM2802015_r1 + + + + + + SRS2561107 + SAMN07730352 + GSM2802015 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237381 + + GSM2802014: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561106 + GSM2802014 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802014 + + + + + + + GEO Accession + GSM2802014 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561106 + SAMN07730560 + GSM2802014 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561106 + SAMN07730560 + GSM2802014 + + + + + + + SRR6124728 + GSM2802014_r1 + + + + + + SRS2561106 + SAMN07730560 + GSM2802014 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237380 + + GSM2802013: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561105 + GSM2802013 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802013 + + + + + + + GEO Accession + GSM2802013 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561105 + SAMN07730561 + GSM2802013 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561105 + SAMN07730561 + GSM2802013 + + + + + + + SRR6124727 + GSM2802013_r1 + + + + + + SRS2561105 + SAMN07730561 + GSM2802013 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237379 + + GSM2802012: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561103 + GSM2802012 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802012 + + + + + + + GEO Accession + GSM2802012 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561103 + SAMN07730562 + GSM2802012 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561103 + SAMN07730562 + GSM2802012 + + + + + + + SRR6124726 + GSM2802012_r1 + + + + + + SRS2561103 + SAMN07730562 + GSM2802012 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237378 + + GSM2802011: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561102 + GSM2802011 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802011 + + + + + + + GEO Accession + GSM2802011 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561102 + SAMN07730563 + GSM2802011 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561102 + SAMN07730563 + GSM2802011 + + + + + + + SRR6124725 + GSM2802011_r1 + + + + + + SRS2561102 + SAMN07730563 + GSM2802011 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237377 + + GSM2802010: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561101 + GSM2802010 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802010 + + + + + + + GEO Accession + GSM2802010 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561101 + SAMN07730564 + GSM2802010 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561101 + SAMN07730564 + GSM2802010 + + + + + + + SRR6124724 + GSM2802010_r1 + + + + + + SRS2561101 + SAMN07730564 + GSM2802010 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237376 + + GSM2802009: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561100 + GSM2802009 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802009 + + + + + + + GEO Accession + GSM2802009 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561100 + SAMN07730565 + GSM2802009 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561100 + SAMN07730565 + GSM2802009 + + + + + + + SRR6124723 + GSM2802009_r1 + + + + + + SRS2561100 + SAMN07730565 + GSM2802009 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237375 + + GSM2802008: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561099 + GSM2802008 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802008 + + + + + + + GEO Accession + GSM2802008 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561099 + SAMN07730566 + GSM2802008 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561099 + SAMN07730566 + GSM2802008 + + + + + + + SRR6124722 + GSM2802008_r1 + + + + + + SRS2561099 + SAMN07730566 + GSM2802008 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237374 + + GSM2802007: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561098 + GSM2802007 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802007 + + + + + + + GEO Accession + GSM2802007 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561098 + SAMN07730567 + GSM2802007 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561098 + SAMN07730567 + GSM2802007 + + + + + + + SRR6124721 + GSM2802007_r1 + + + + + + SRS2561098 + SAMN07730567 + GSM2802007 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237373 + + GSM2802006: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561097 + GSM2802006 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802006 + + + + + + + GEO Accession + GSM2802006 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561097 + SAMN07730568 + GSM2802006 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561097 + SAMN07730568 + GSM2802006 + + + + + + + SRR6124720 + GSM2802006_r1 + + + + + + SRS2561097 + SAMN07730568 + GSM2802006 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237372 + + GSM2802005: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561096 + GSM2802005 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802005 + + + + + + + GEO Accession + GSM2802005 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561096 + SAMN07730569 + GSM2802005 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561096 + SAMN07730569 + GSM2802005 + + + + + + + SRR6124719 + GSM2802005_r1 + + + + + + SRS2561096 + SAMN07730569 + GSM2802005 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237371 + + GSM2802004: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561095 + GSM2802004 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802004 + + + + + + + GEO Accession + GSM2802004 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561095 + SAMN07730570 + GSM2802004 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561095 + SAMN07730570 + GSM2802004 + + + + + + + SRR6124718 + GSM2802004_r1 + + + + + + SRS2561095 + SAMN07730570 + GSM2802004 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237370 + + GSM2802003: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561094 + GSM2802003 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802003 + + + + + + + GEO Accession + GSM2802003 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561094 + SAMN07730575 + GSM2802003 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561094 + SAMN07730575 + GSM2802003 + + + + + + + SRR6124717 + GSM2802003_r1 + + + + + + SRS2561094 + SAMN07730575 + GSM2802003 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237369 + + GSM2802002: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561093 + GSM2802002 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802002 + + + + + + + GEO Accession + GSM2802002 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561093 + SAMN07730576 + GSM2802002 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561093 + SAMN07730576 + GSM2802002 + + + + + + + SRR6124716 + GSM2802002_r1 + + + + + + SRS2561093 + SAMN07730576 + GSM2802002 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237368 + + GSM2802001: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561092 + GSM2802001 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802001 + + + + + + + GEO Accession + GSM2802001 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561092 + SAMN07730571 + GSM2802001 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561092 + SAMN07730571 + GSM2802001 + + + + + + + SRR6124715 + GSM2802001_r1 + + + + + + SRS2561092 + SAMN07730571 + GSM2802001 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237367 + + GSM2802000: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561089 + GSM2802000 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302802000 + + + + + + + GEO Accession + GSM2802000 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561089 + SAMN07730572 + GSM2802000 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561089 + SAMN07730572 + GSM2802000 + + + + + + + SRR6124714 + GSM2802000_r1 + + + + + + SRS2561089 + SAMN07730572 + GSM2802000 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237366 + + GSM2801999: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561091 + GSM2801999 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801999 + + + + + + + GEO Accession + GSM2801999 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561091 + SAMN07730573 + GSM2801999 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561091 + SAMN07730573 + GSM2801999 + + + + + + + SRR6124713 + GSM2801999_r1 + + + + + + SRS2561091 + SAMN07730573 + GSM2801999 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237365 + + GSM2801998: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561090 + GSM2801998 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801998 + + + + + + + GEO Accession + GSM2801998 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561090 + SAMN07730574 + GSM2801998 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561090 + SAMN07730574 + GSM2801998 + + + + + + + SRR6124712 + GSM2801998_r1 + + + + + + SRS2561090 + SAMN07730574 + GSM2801998 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237364 + + GSM2801997: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561193 + GSM2801997 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801997 + + + + + + + GEO Accession + GSM2801997 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561193 + SAMN07730577 + GSM2801997 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561193 + SAMN07730577 + GSM2801997 + + + + + + + SRR6124711 + GSM2801997_r1 + + + + + + SRS2561193 + SAMN07730577 + GSM2801997 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237363 + + GSM2801996: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561088 + GSM2801996 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801996 + + + + + + + GEO Accession + GSM2801996 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561088 + SAMN07730578 + GSM2801996 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561088 + SAMN07730578 + GSM2801996 + + + + + + + SRR6124710 + GSM2801996_r1 + + + + + + SRS2561088 + SAMN07730578 + GSM2801996 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237362 + + GSM2801995: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561087 + GSM2801995 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801995 + + + + + + + GEO Accession + GSM2801995 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561087 + SAMN07730579 + GSM2801995 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561087 + SAMN07730579 + GSM2801995 + + + + + + + SRR6124709 + GSM2801995_r1 + + + + + + SRS2561087 + SAMN07730579 + GSM2801995 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237361 + + GSM2801994: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561086 + GSM2801994 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801994 + + + + + + + GEO Accession + GSM2801994 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561086 + SAMN07730580 + GSM2801994 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561086 + SAMN07730580 + GSM2801994 + + + + + + + SRR6124708 + GSM2801994_r1 + + + + + + SRS2561086 + SAMN07730580 + GSM2801994 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237360 + + GSM2801993: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561085 + GSM2801993 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801993 + + + + + + + GEO Accession + GSM2801993 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561085 + SAMN07730581 + GSM2801993 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561085 + SAMN07730581 + GSM2801993 + + + + + + + SRR6124707 + GSM2801993_r1 + + + + + + SRS2561085 + SAMN07730581 + GSM2801993 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237359 + + GSM2801992: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561084 + GSM2801992 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801992 + + + + + + + GEO Accession + GSM2801992 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561084 + SAMN07730582 + GSM2801992 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561084 + SAMN07730582 + GSM2801992 + + + + + + + SRR6124706 + GSM2801992_r1 + + + + + + SRS2561084 + SAMN07730582 + GSM2801992 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237358 + + GSM2801991: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561082 + GSM2801991 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801991 + + + + + + + GEO Accession + GSM2801991 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561082 + SAMN07730583 + GSM2801991 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561082 + SAMN07730583 + GSM2801991 + + + + + + + SRR6124705 + GSM2801991_r1 + + + + + + SRS2561082 + SAMN07730583 + GSM2801991 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237357 + + GSM2801990: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561083 + GSM2801990 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801990 + + + + + + + GEO Accession + GSM2801990 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561083 + SAMN07730584 + GSM2801990 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561083 + SAMN07730584 + GSM2801990 + + + + + + + SRR6124704 + GSM2801990_r1 + + + + + + SRS2561083 + SAMN07730584 + GSM2801990 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237356 + + GSM2801989: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561081 + GSM2801989 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801989 + + + + + + + GEO Accession + GSM2801989 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561081 + SAMN07730585 + GSM2801989 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561081 + SAMN07730585 + GSM2801989 + + + + + + + SRR6124703 + GSM2801989_r1 + + + + + + SRS2561081 + SAMN07730585 + GSM2801989 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237355 + + GSM2801988: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561078 + GSM2801988 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801988 + + + + + + + GEO Accession + GSM2801988 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561078 + SAMN07730586 + GSM2801988 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561078 + SAMN07730586 + GSM2801988 + + + + + + + SRR6124702 + GSM2801988_r1 + + + + + + SRS2561078 + SAMN07730586 + GSM2801988 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237354 + + GSM2801987: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561080 + GSM2801987 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801987 + + + + + + + GEO Accession + GSM2801987 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561080 + SAMN07730587 + GSM2801987 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561080 + SAMN07730587 + GSM2801987 + + + + + + + SRR6124701 + GSM2801987_r1 + + + + + + SRS2561080 + SAMN07730587 + GSM2801987 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237353 + + GSM2801986: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561079 + GSM2801986 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801986 + + + + + + + GEO Accession + GSM2801986 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561079 + SAMN07730588 + GSM2801986 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561079 + SAMN07730588 + GSM2801986 + + + + + + + SRR6124700 + GSM2801986_r1 + + + + + + SRS2561079 + SAMN07730588 + GSM2801986 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237352 + + GSM2801985: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561077 + GSM2801985 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801985 + + + + + + + GEO Accession + GSM2801985 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561077 + SAMN07730589 + GSM2801985 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561077 + SAMN07730589 + GSM2801985 + + + + + + + SRR6124699 + GSM2801985_r1 + + + + + + SRS2561077 + SAMN07730589 + GSM2801985 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237351 + + GSM2801984: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561076 + GSM2801984 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801984 + + + + + + + GEO Accession + GSM2801984 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561076 + SAMN07730590 + GSM2801984 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561076 + SAMN07730590 + GSM2801984 + + + + + + + SRR6124698 + GSM2801984_r1 + + + + + + SRS2561076 + SAMN07730590 + GSM2801984 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237350 + + GSM2801983: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561075 + GSM2801983 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801983 + + + + + + + GEO Accession + GSM2801983 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561075 + SAMN07730591 + GSM2801983 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561075 + SAMN07730591 + GSM2801983 + + + + + + + SRR6124697 + GSM2801983_r1 + + + + + + SRS2561075 + SAMN07730591 + GSM2801983 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237349 + + GSM2801982: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561074 + GSM2801982 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801982 + + + + + + + GEO Accession + GSM2801982 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561074 + SAMN07730592 + GSM2801982 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561074 + SAMN07730592 + GSM2801982 + + + + + + + SRR6124696 + GSM2801982_r1 + + + + + + SRS2561074 + SAMN07730592 + GSM2801982 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237348 + + GSM2801981: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561073 + GSM2801981 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801981 + + + + + + + GEO Accession + GSM2801981 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561073 + SAMN07729963 + GSM2801981 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561073 + SAMN07729963 + GSM2801981 + + + + + + + SRR6124695 + GSM2801981_r1 + + + + + + SRS2561073 + SAMN07729963 + GSM2801981 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237347 + + GSM2801980: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561072 + GSM2801980 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801980 + + + + + + + GEO Accession + GSM2801980 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561072 + SAMN07729964 + GSM2801980 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561072 + SAMN07729964 + GSM2801980 + + + + + + + SRR6124694 + GSM2801980_r1 + + + + + + SRS2561072 + SAMN07729964 + GSM2801980 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237346 + + GSM2801979: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561069 + GSM2801979 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801979 + + + + + + + GEO Accession + GSM2801979 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561069 + SAMN07729965 + GSM2801979 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561069 + SAMN07729965 + GSM2801979 + + + + + + + SRR6124693 + GSM2801979_r1 + + + + + + SRS2561069 + SAMN07729965 + GSM2801979 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237345 + + GSM2801978: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561070 + GSM2801978 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801978 + + + + + + + GEO Accession + GSM2801978 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561070 + SAMN07729966 + GSM2801978 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561070 + SAMN07729966 + GSM2801978 + + + + + + + SRR6124692 + GSM2801978_r1 + + + + + + SRS2561070 + SAMN07729966 + GSM2801978 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237344 + + GSM2801977: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561068 + GSM2801977 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801977 + + + + + + + GEO Accession + GSM2801977 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561068 + SAMN07729967 + GSM2801977 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561068 + SAMN07729967 + GSM2801977 + + + + + + + SRR6124691 + GSM2801977_r1 + + + + + + SRS2561068 + SAMN07729967 + GSM2801977 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237343 + + GSM2801976: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561067 + GSM2801976 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801976 + + + + + + + GEO Accession + GSM2801976 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561067 + SAMN07729968 + GSM2801976 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561067 + SAMN07729968 + GSM2801976 + + + + + + + SRR6124690 + GSM2801976_r1 + + + + + + SRS2561067 + SAMN07729968 + GSM2801976 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237342 + + GSM2801975: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561066 + GSM2801975 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801975 + + + + + + + GEO Accession + GSM2801975 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561066 + SAMN07729969 + GSM2801975 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561066 + SAMN07729969 + GSM2801975 + + + + + + + SRR6124689 + GSM2801975_r1 + + + + + + SRS2561066 + SAMN07729969 + GSM2801975 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237341 + + GSM2801974: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561065 + GSM2801974 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801974 + + + + + + + GEO Accession + GSM2801974 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561065 + SAMN07729970 + GSM2801974 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561065 + SAMN07729970 + GSM2801974 + + + + + + + SRR6124688 + GSM2801974_r1 + + + + + + SRS2561065 + SAMN07729970 + GSM2801974 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237340 + + GSM2801973: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561064 + GSM2801973 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801973 + + + + + + + GEO Accession + GSM2801973 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561064 + SAMN07729971 + GSM2801973 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561064 + SAMN07729971 + GSM2801973 + + + + + + + SRR6124687 + GSM2801973_r1 + + + + + + SRS2561064 + SAMN07729971 + GSM2801973 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237339 + + GSM2801972: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561063 + GSM2801972 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801972 + + + + + + + GEO Accession + GSM2801972 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561063 + SAMN07729972 + GSM2801972 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561063 + SAMN07729972 + GSM2801972 + + + + + + + SRR6124686 + GSM2801972_r1 + + + + + + SRS2561063 + SAMN07729972 + GSM2801972 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237338 + + GSM2801971: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561062 + GSM2801971 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801971 + + + + + + + GEO Accession + GSM2801971 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561062 + SAMN07729973 + GSM2801971 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561062 + SAMN07729973 + GSM2801971 + + + + + + + SRR6124685 + GSM2801971_r1 + + + + + + SRS2561062 + SAMN07729973 + GSM2801971 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237337 + + GSM2801970: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561059 + GSM2801970 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801970 + + + + + + + GEO Accession + GSM2801970 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561059 + SAMN07729974 + GSM2801970 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561059 + SAMN07729974 + GSM2801970 + + + + + + + SRR6124684 + GSM2801970_r1 + + + + + + SRS2561059 + SAMN07729974 + GSM2801970 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237336 + + GSM2801969: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561061 + GSM2801969 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801969 + + + + + + + GEO Accession + GSM2801969 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561061 + SAMN07729975 + GSM2801969 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561061 + SAMN07729975 + GSM2801969 + + + + + + + SRR6124683 + GSM2801969_r1 + + + + + + SRS2561061 + SAMN07729975 + GSM2801969 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237335 + + GSM2801968: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561060 + GSM2801968 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801968 + + + + + + + GEO Accession + GSM2801968 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561060 + SAMN07729976 + GSM2801968 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561060 + SAMN07729976 + GSM2801968 + + + + + + + SRR6124682 + GSM2801968_r1 + + + + + + SRS2561060 + SAMN07729976 + GSM2801968 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237334 + + GSM2801967: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561058 + GSM2801967 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801967 + + + + + + + GEO Accession + GSM2801967 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561058 + SAMN07729977 + GSM2801967 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561058 + SAMN07729977 + GSM2801967 + + + + + + + SRR6124681 + GSM2801967_r1 + + + + + + SRS2561058 + SAMN07729977 + GSM2801967 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237333 + + GSM2801966: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561056 + GSM2801966 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801966 + + + + + + + GEO Accession + GSM2801966 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561056 + SAMN07729978 + GSM2801966 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561056 + SAMN07729978 + GSM2801966 + + + + + + + SRR6124680 + GSM2801966_r1 + + + + + + SRS2561056 + SAMN07729978 + GSM2801966 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237332 + + GSM2801965: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561057 + GSM2801965 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801965 + + + + + + + GEO Accession + GSM2801965 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561057 + SAMN07729979 + GSM2801965 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561057 + SAMN07729979 + GSM2801965 + + + + + + + SRR6124679 + GSM2801965_r1 + + + + + + SRS2561057 + SAMN07729979 + GSM2801965 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237331 + + GSM2801964: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561150 + GSM2801964 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801964 + + + + + + + GEO Accession + GSM2801964 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561150 + SAMN07729980 + GSM2801964 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561150 + SAMN07729980 + GSM2801964 + + + + + + + SRR6124678 + GSM2801964_r1 + + + + + + SRS2561150 + SAMN07729980 + GSM2801964 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237330 + + GSM2801963: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561055 + GSM2801963 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801963 + + + + + + + GEO Accession + GSM2801963 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561055 + SAMN07729981 + GSM2801963 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561055 + SAMN07729981 + GSM2801963 + + + + + + + SRR6124677 + GSM2801963_r1 + + + + + + SRS2561055 + SAMN07729981 + GSM2801963 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237329 + + GSM2801962: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561054 + GSM2801962 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801962 + + + + + + + GEO Accession + GSM2801962 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561054 + SAMN07729982 + GSM2801962 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561054 + SAMN07729982 + GSM2801962 + + + + + + + SRR6124676 + GSM2801962_r1 + + + + + + SRS2561054 + SAMN07729982 + GSM2801962 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237328 + + GSM2801961: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561053 + GSM2801961 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801961 + + + + + + + GEO Accession + GSM2801961 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561053 + SAMN07729983 + GSM2801961 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561053 + SAMN07729983 + GSM2801961 + + + + + + + SRR6124675 + GSM2801961_r1 + + + + + + SRS2561053 + SAMN07729983 + GSM2801961 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237327 + + GSM2801960: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561052 + GSM2801960 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801960 + + + + + + + GEO Accession + GSM2801960 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561052 + SAMN07729984 + GSM2801960 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561052 + SAMN07729984 + GSM2801960 + + + + + + + SRR6124674 + GSM2801960_r1 + + + + + + SRS2561052 + SAMN07729984 + GSM2801960 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237326 + + GSM2801959: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561051 + GSM2801959 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801959 + + + + + + + GEO Accession + GSM2801959 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561051 + SAMN07729985 + GSM2801959 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561051 + SAMN07729985 + GSM2801959 + + + + + + + SRR6124673 + GSM2801959_r1 + + + + + + SRS2561051 + SAMN07729985 + GSM2801959 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237325 + + GSM2801958: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561050 + GSM2801958 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801958 + + + + + + + GEO Accession + GSM2801958 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561050 + SAMN07729986 + GSM2801958 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561050 + SAMN07729986 + GSM2801958 + + + + + + + SRR6124672 + GSM2801958_r1 + + + + + + SRS2561050 + SAMN07729986 + GSM2801958 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237324 + + GSM2801957: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561048 + GSM2801957 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801957 + + + + + + + GEO Accession + GSM2801957 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561048 + SAMN07729987 + GSM2801957 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561048 + SAMN07729987 + GSM2801957 + + + + + + + SRR6124671 + GSM2801957_r1 + + + + + + SRS2561048 + SAMN07729987 + GSM2801957 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237323 + + GSM2801956: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561049 + GSM2801956 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801956 + + + + + + + GEO Accession + GSM2801956 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561049 + SAMN07729988 + GSM2801956 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561049 + SAMN07729988 + GSM2801956 + + + + + + + SRR6124670 + GSM2801956_r1 + + + + + + SRS2561049 + SAMN07729988 + GSM2801956 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237322 + + GSM2801955: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561047 + GSM2801955 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801955 + + + + + + + GEO Accession + GSM2801955 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561047 + SAMN07729989 + GSM2801955 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561047 + SAMN07729989 + GSM2801955 + + + + + + + SRR6124669 + GSM2801955_r1 + + + + + + SRS2561047 + SAMN07729989 + GSM2801955 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237321 + + GSM2801954: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561046 + GSM2801954 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801954 + + + + + + + GEO Accession + GSM2801954 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561046 + SAMN07729990 + GSM2801954 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561046 + SAMN07729990 + GSM2801954 + + + + + + + SRR6124668 + GSM2801954_r1 + + + + + + SRS2561046 + SAMN07729990 + GSM2801954 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237320 + + GSM2801953: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561045 + GSM2801953 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801953 + + + + + + + GEO Accession + GSM2801953 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561045 + SAMN07729991 + GSM2801953 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561045 + SAMN07729991 + GSM2801953 + + + + + + + SRR6124667 + GSM2801953_r1 + + + + + + SRS2561045 + SAMN07729991 + GSM2801953 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237319 + + GSM2801952: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561044 + GSM2801952 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801952 + + + + + + + GEO Accession + GSM2801952 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561044 + SAMN07729992 + GSM2801952 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561044 + SAMN07729992 + GSM2801952 + + + + + + + SRR6124666 + GSM2801952_r1 + + + + + + SRS2561044 + SAMN07729992 + GSM2801952 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237318 + + GSM2801951: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561043 + GSM2801951 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801951 + + + + + + + GEO Accession + GSM2801951 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561043 + SAMN07729993 + GSM2801951 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561043 + SAMN07729993 + GSM2801951 + + + + + + + SRR6124665 + GSM2801951_r1 + + + + + + SRS2561043 + SAMN07729993 + GSM2801951 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237317 + + GSM2801950: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561042 + GSM2801950 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801950 + + + + + + + GEO Accession + GSM2801950 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561042 + SAMN07729994 + GSM2801950 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561042 + SAMN07729994 + GSM2801950 + + + + + + + SRR6124664 + GSM2801950_r1 + + + + + + SRS2561042 + SAMN07729994 + GSM2801950 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237316 + + GSM2801949: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561041 + GSM2801949 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801949 + + + + + + + GEO Accession + GSM2801949 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561041 + SAMN07729995 + GSM2801949 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561041 + SAMN07729995 + GSM2801949 + + + + + + + SRR6124663 + GSM2801949_r1 + + + + + + SRS2561041 + SAMN07729995 + GSM2801949 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237315 + + GSM2801948: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561040 + GSM2801948 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801948 + + + + + + + GEO Accession + GSM2801948 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561040 + SAMN07729996 + GSM2801948 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561040 + SAMN07729996 + GSM2801948 + + + + + + + SRR6124662 + GSM2801948_r1 + + + + + + SRS2561040 + SAMN07729996 + GSM2801948 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237314 + + GSM2801947: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561039 + GSM2801947 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801947 + + + + + + + GEO Accession + GSM2801947 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561039 + SAMN07729997 + GSM2801947 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561039 + SAMN07729997 + GSM2801947 + + + + + + + SRR6124661 + GSM2801947_r1 + + + + + + SRS2561039 + SAMN07729997 + GSM2801947 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237313 + + GSM2801946: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561038 + GSM2801946 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801946 + + + + + + + GEO Accession + GSM2801946 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561038 + SAMN07729998 + GSM2801946 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561038 + SAMN07729998 + GSM2801946 + + + + + + + SRR6124660 + GSM2801946_r1 + + + + + + SRS2561038 + SAMN07729998 + GSM2801946 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237312 + + GSM2801945: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561037 + GSM2801945 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801945 + + + + + + + GEO Accession + GSM2801945 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561037 + SAMN07729999 + GSM2801945 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561037 + SAMN07729999 + GSM2801945 + + + + + + + SRR6124659 + GSM2801945_r1 + + + + + + SRS2561037 + SAMN07729999 + GSM2801945 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237311 + + GSM2801944: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561036 + GSM2801944 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801944 + + + + + + + GEO Accession + GSM2801944 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561036 + SAMN07730000 + GSM2801944 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561036 + SAMN07730000 + GSM2801944 + + + + + + + SRR6124658 + GSM2801944_r1 + + + + + + SRS2561036 + SAMN07730000 + GSM2801944 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237310 + + GSM2801943: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561035 + GSM2801943 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801943 + + + + + + + GEO Accession + GSM2801943 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561035 + SAMN07730001 + GSM2801943 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561035 + SAMN07730001 + GSM2801943 + + + + + + + SRR6124657 + GSM2801943_r1 + + + + + + SRS2561035 + SAMN07730001 + GSM2801943 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237309 + + GSM2801942: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561034 + GSM2801942 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801942 + + + + + + + GEO Accession + GSM2801942 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561034 + SAMN07730005 + GSM2801942 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561034 + SAMN07730005 + GSM2801942 + + + + + + + SRR6124656 + GSM2801942_r1 + + + + + + SRS2561034 + SAMN07730005 + GSM2801942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237308 + + GSM2801941: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561033 + GSM2801941 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801941 + + + + + + + GEO Accession + GSM2801941 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561033 + SAMN07730002 + GSM2801941 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561033 + SAMN07730002 + GSM2801941 + + + + + + + SRR6124655 + GSM2801941_r1 + + + + + + SRS2561033 + SAMN07730002 + GSM2801941 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237307 + + GSM2801940: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561032 + GSM2801940 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801940 + + + + + + + GEO Accession + GSM2801940 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561032 + SAMN07730003 + GSM2801940 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561032 + SAMN07730003 + GSM2801940 + + + + + + + SRR6124654 + GSM2801940_r1 + + + + + + SRS2561032 + SAMN07730003 + GSM2801940 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237306 + + GSM2801939: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561031 + GSM2801939 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801939 + + + + + + + GEO Accession + GSM2801939 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561031 + SAMN07730004 + GSM2801939 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561031 + SAMN07730004 + GSM2801939 + + + + + + + SRR6124653 + GSM2801939_r1 + + + + + + SRS2561031 + SAMN07730004 + GSM2801939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237305 + + GSM2801938: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561030 + GSM2801938 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801938 + + + + + + + GEO Accession + GSM2801938 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561030 + SAMN07730006 + GSM2801938 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561030 + SAMN07730006 + GSM2801938 + + + + + + + SRR6124652 + GSM2801938_r1 + + + + + + SRS2561030 + SAMN07730006 + GSM2801938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237304 + + GSM2801937: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561029 + GSM2801937 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801937 + + + + + + + GEO Accession + GSM2801937 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561029 + SAMN07730007 + GSM2801937 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561029 + SAMN07730007 + GSM2801937 + + + + + + + SRR6124651 + GSM2801937_r1 + + + + + + SRS2561029 + SAMN07730007 + GSM2801937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237303 + + GSM2801936: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561028 + GSM2801936 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801936 + + + + + + + GEO Accession + GSM2801936 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561028 + SAMN07730008 + GSM2801936 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561028 + SAMN07730008 + GSM2801936 + + + + + + + SRR6124650 + GSM2801936_r1 + + + + + + SRS2561028 + SAMN07730008 + GSM2801936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237302 + + GSM2801935: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561027 + GSM2801935 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801935 + + + + + + + GEO Accession + GSM2801935 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561027 + SAMN07730009 + GSM2801935 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561027 + SAMN07730009 + GSM2801935 + + + + + + + SRR6124649 + GSM2801935_r1 + + + + + + SRS2561027 + SAMN07730009 + GSM2801935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237301 + + GSM2801934: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561026 + GSM2801934 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801934 + + + + + + + GEO Accession + GSM2801934 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561026 + SAMN07730010 + GSM2801934 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561026 + SAMN07730010 + GSM2801934 + + + + + + + SRR6124648 + GSM2801934_r1 + + + + + + SRS2561026 + SAMN07730010 + GSM2801934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237300 + + GSM2801933: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561025 + GSM2801933 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801933 + + + + + + + GEO Accession + GSM2801933 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561025 + SAMN07730011 + GSM2801933 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561025 + SAMN07730011 + GSM2801933 + + + + + + + SRR6124647 + GSM2801933_r1 + + + + + + SRS2561025 + SAMN07730011 + GSM2801933 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237299 + + GSM2801932: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561024 + GSM2801932 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801932 + + + + + + + GEO Accession + GSM2801932 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561024 + SAMN07730012 + GSM2801932 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561024 + SAMN07730012 + GSM2801932 + + + + + + + SRR6124646 + GSM2801932_r1 + + + + + + SRS2561024 + SAMN07730012 + GSM2801932 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237298 + + GSM2801931: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561023 + GSM2801931 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801931 + + + + + + + GEO Accession + GSM2801931 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561023 + SAMN07730013 + GSM2801931 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561023 + SAMN07730013 + GSM2801931 + + + + + + + SRR6124645 + GSM2801931_r1 + + + + + + SRS2561023 + SAMN07730013 + GSM2801931 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237297 + + GSM2801930: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561022 + GSM2801930 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801930 + + + + + + + GEO Accession + GSM2801930 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561022 + SAMN07730014 + GSM2801930 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561022 + SAMN07730014 + GSM2801930 + + + + + + + SRR6124644 + GSM2801930_r1 + + + + + + SRS2561022 + SAMN07730014 + GSM2801930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237296 + + GSM2801929: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561021 + GSM2801929 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801929 + + + + + + + GEO Accession + GSM2801929 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561021 + SAMN07730015 + GSM2801929 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561021 + SAMN07730015 + GSM2801929 + + + + + + + SRR6124643 + GSM2801929_r1 + + + + + + SRS2561021 + SAMN07730015 + GSM2801929 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237295 + + GSM2801928: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561020 + GSM2801928 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801928 + + + + + + + GEO Accession + GSM2801928 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561020 + SAMN07730016 + GSM2801928 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561020 + SAMN07730016 + GSM2801928 + + + + + + + SRR6124642 + GSM2801928_r1 + + + + + + SRS2561020 + SAMN07730016 + GSM2801928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237294 + + GSM2801927: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561019 + GSM2801927 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801927 + + + + + + + GEO Accession + GSM2801927 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561019 + SAMN07730017 + GSM2801927 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561019 + SAMN07730017 + GSM2801927 + + + + + + + SRR6124641 + GSM2801927_r1 + + + + + + SRS2561019 + SAMN07730017 + GSM2801927 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237293 + + GSM2801926: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561018 + GSM2801926 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801926 + + + + + + + GEO Accession + GSM2801926 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561018 + SAMN07730018 + GSM2801926 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561018 + SAMN07730018 + GSM2801926 + + + + + + + SRR6124640 + GSM2801926_r1 + + + + + + SRS2561018 + SAMN07730018 + GSM2801926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237292 + + GSM2801925: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561017 + GSM2801925 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801925 + + + + + + + GEO Accession + GSM2801925 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561017 + SAMN07730019 + GSM2801925 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561017 + SAMN07730019 + GSM2801925 + + + + + + + SRR6124639 + GSM2801925_r1 + + + + + + SRS2561017 + SAMN07730019 + GSM2801925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237291 + + GSM2801924: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561016 + GSM2801924 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801924 + + + + + + + GEO Accession + GSM2801924 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561016 + SAMN07730020 + GSM2801924 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561016 + SAMN07730020 + GSM2801924 + + + + + + + SRR6124638 + GSM2801924_r1 + + + + + + SRS2561016 + SAMN07730020 + GSM2801924 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237290 + + GSM2801923: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561015 + GSM2801923 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801923 + + + + + + + GEO Accession + GSM2801923 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561015 + SAMN07730021 + GSM2801923 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561015 + SAMN07730021 + GSM2801923 + + + + + + + SRR6124637 + GSM2801923_r1 + + + + + + SRS2561015 + SAMN07730021 + GSM2801923 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237289 + + GSM2801922: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561014 + GSM2801922 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801922 + + + + + + + GEO Accession + GSM2801922 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561014 + SAMN07730022 + GSM2801922 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561014 + SAMN07730022 + GSM2801922 + + + + + + + SRR6124636 + GSM2801922_r1 + + + + + + SRS2561014 + SAMN07730022 + GSM2801922 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237288 + + GSM2801921: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561012 + GSM2801921 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801921 + + + + + + + GEO Accession + GSM2801921 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561012 + SAMN07730023 + GSM2801921 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561012 + SAMN07730023 + GSM2801921 + + + + + + + SRR6124635 + GSM2801921_r1 + + + + + + SRS2561012 + SAMN07730023 + GSM2801921 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237287 + + GSM2801920: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561013 + GSM2801920 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801920 + + + + + + + GEO Accession + GSM2801920 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561013 + SAMN07730024 + GSM2801920 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561013 + SAMN07730024 + GSM2801920 + + + + + + + SRR6124634 + GSM2801920_r1 + + + + + + SRS2561013 + SAMN07730024 + GSM2801920 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237286 + + GSM2801919: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561011 + GSM2801919 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801919 + + + + + + + GEO Accession + GSM2801919 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561011 + SAMN07730025 + GSM2801919 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561011 + SAMN07730025 + GSM2801919 + + + + + + + SRR6124633 + GSM2801919_r1 + + + + + + SRS2561011 + SAMN07730025 + GSM2801919 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237285 + + GSM2801918: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561010 + GSM2801918 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801918 + + + + + + + GEO Accession + GSM2801918 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561010 + SAMN07730026 + GSM2801918 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561010 + SAMN07730026 + GSM2801918 + + + + + + + SRR6124632 + GSM2801918_r1 + + + + + + SRS2561010 + SAMN07730026 + GSM2801918 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237284 + + GSM2801917: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561104 + GSM2801917 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801917 + + + + + + + GEO Accession + GSM2801917 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561104 + SAMN07730027 + GSM2801917 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561104 + SAMN07730027 + GSM2801917 + + + + + + + SRR6124631 + GSM2801917_r1 + + + + + + SRS2561104 + SAMN07730027 + GSM2801917 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237283 + + GSM2801916: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561009 + GSM2801916 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801916 + + + + + + + GEO Accession + GSM2801916 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561009 + SAMN07730028 + GSM2801916 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561009 + SAMN07730028 + GSM2801916 + + + + + + + SRR6124630 + GSM2801916_r1 + + + + + + SRS2561009 + SAMN07730028 + GSM2801916 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237282 + + GSM2801915: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561008 + GSM2801915 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801915 + + + + + + + GEO Accession + GSM2801915 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561008 + SAMN07730029 + GSM2801915 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561008 + SAMN07730029 + GSM2801915 + + + + + + + SRR6124629 + GSM2801915_r1 + + + + + + SRS2561008 + SAMN07730029 + GSM2801915 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237281 + + GSM2801914: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561007 + GSM2801914 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801914 + + + + + + + GEO Accession + GSM2801914 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561007 + SAMN07730030 + GSM2801914 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561007 + SAMN07730030 + GSM2801914 + + + + + + + SRR6124628 + GSM2801914_r1 + + + + + + SRS2561007 + SAMN07730030 + GSM2801914 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237280 + + GSM2801913: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561006 + GSM2801913 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801913 + + + + + + + GEO Accession + GSM2801913 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561006 + SAMN07730031 + GSM2801913 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561006 + SAMN07730031 + GSM2801913 + + + + + + + SRR6124627 + GSM2801913_r1 + + + + + + SRS2561006 + SAMN07730031 + GSM2801913 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237279 + + GSM2801912: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561005 + GSM2801912 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801912 + + + + + + + GEO Accession + GSM2801912 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561005 + SAMN07730032 + GSM2801912 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561005 + SAMN07730032 + GSM2801912 + + + + + + + SRR6124626 + GSM2801912_r1 + + + + + + SRS2561005 + SAMN07730032 + GSM2801912 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237278 + + GSM2801911: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561004 + GSM2801911 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801911 + + + + + + + GEO Accession + GSM2801911 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561004 + SAMN07730033 + GSM2801911 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561004 + SAMN07730033 + GSM2801911 + + + + + + + SRR6124625 + GSM2801911_r1 + + + + + + SRS2561004 + SAMN07730033 + GSM2801911 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237277 + + GSM2801910: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561003 + GSM2801910 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801910 + + + + + + + GEO Accession + GSM2801910 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561003 + SAMN07730034 + GSM2801910 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561003 + SAMN07730034 + GSM2801910 + + + + + + + SRR6124624 + GSM2801910_r1 + + + + + + SRS2561003 + SAMN07730034 + GSM2801910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237276 + + GSM2801909: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561001 + GSM2801909 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801909 + + + + + + + GEO Accession + GSM2801909 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561001 + SAMN07730035 + GSM2801909 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561001 + SAMN07730035 + GSM2801909 + + + + + + + SRR6124623 + GSM2801909_r1 + + + + + + SRS2561001 + SAMN07730035 + GSM2801909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237275 + + GSM2801908: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561000 + GSM2801908 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801908 + + + + + + + GEO Accession + GSM2801908 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561000 + SAMN07730036 + GSM2801908 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561000 + SAMN07730036 + GSM2801908 + + + + + + + SRR6124622 + GSM2801908_r1 + + + + + + SRS2561000 + SAMN07730036 + GSM2801908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237274 + + GSM2801907: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560999 + GSM2801907 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801907 + + + + + + + GEO Accession + GSM2801907 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560999 + SAMN07730037 + GSM2801907 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560999 + SAMN07730037 + GSM2801907 + + + + + + + SRR6124621 + GSM2801907_r1 + + + + + + SRS2560999 + SAMN07730037 + GSM2801907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237273 + + GSM2801906: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560998 + GSM2801906 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801906 + + + + + + + GEO Accession + GSM2801906 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560998 + SAMN07730038 + GSM2801906 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560998 + SAMN07730038 + GSM2801906 + + + + + + + SRR6124620 + GSM2801906_r1 + + + + + + SRS2560998 + SAMN07730038 + GSM2801906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237272 + + GSM2801905: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560997 + GSM2801905 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801905 + + + + + + + GEO Accession + GSM2801905 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560997 + SAMN07730039 + GSM2801905 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560997 + SAMN07730039 + GSM2801905 + + + + + + + SRR6124619 + GSM2801905_r1 + + + + + + SRS2560997 + SAMN07730039 + GSM2801905 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237271 + + GSM2801904: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560996 + GSM2801904 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801904 + + + + + + + GEO Accession + GSM2801904 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560996 + SAMN07730040 + GSM2801904 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560996 + SAMN07730040 + GSM2801904 + + + + + + + SRR6124618 + GSM2801904_r1 + + + + + + SRS2560996 + SAMN07730040 + GSM2801904 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237270 + + GSM2801903: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560995 + GSM2801903 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801903 + + + + + + + GEO Accession + GSM2801903 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560995 + SAMN07730041 + GSM2801903 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560995 + SAMN07730041 + GSM2801903 + + + + + + + SRR6124617 + GSM2801903_r1 + + + + + + SRS2560995 + SAMN07730041 + GSM2801903 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237269 + + GSM2801902: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560994 + GSM2801902 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801902 + + + + + + + GEO Accession + GSM2801902 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560994 + SAMN07730042 + GSM2801902 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560994 + SAMN07730042 + GSM2801902 + + + + + + + SRR6124616 + GSM2801902_r1 + + + + + + SRS2560994 + SAMN07730042 + GSM2801902 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237268 + + GSM2801901: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560993 + GSM2801901 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801901 + + + + + + + GEO Accession + GSM2801901 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560993 + SAMN07730043 + GSM2801901 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560993 + SAMN07730043 + GSM2801901 + + + + + + + SRR6124615 + GSM2801901_r1 + + + + + + SRS2560993 + SAMN07730043 + GSM2801901 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237267 + + GSM2801900: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560991 + GSM2801900 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801900 + + + + + + + GEO Accession + GSM2801900 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560991 + SAMN07730044 + GSM2801900 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560991 + SAMN07730044 + GSM2801900 + + + + + + + SRR6124614 + GSM2801900_r1 + + + + + + SRS2560991 + SAMN07730044 + GSM2801900 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237266 + + GSM2801899: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560992 + GSM2801899 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801899 + + + + + + + GEO Accession + GSM2801899 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560992 + SAMN07730045 + GSM2801899 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560992 + SAMN07730045 + GSM2801899 + + + + + + + SRR6124613 + GSM2801899_r1 + + + + + + SRS2560992 + SAMN07730045 + GSM2801899 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237265 + + GSM2801898: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560990 + GSM2801898 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801898 + + + + + + + GEO Accession + GSM2801898 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560990 + SAMN07730046 + GSM2801898 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560990 + SAMN07730046 + GSM2801898 + + + + + + + SRR6124612 + GSM2801898_r1 + + + + + + SRS2560990 + SAMN07730046 + GSM2801898 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237264 + + GSM2801897: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560988 + GSM2801897 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801897 + + + + + + + GEO Accession + GSM2801897 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560988 + SAMN07730047 + GSM2801897 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560988 + SAMN07730047 + GSM2801897 + + + + + + + SRR6124611 + GSM2801897_r1 + + + + + + SRS2560988 + SAMN07730047 + GSM2801897 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237263 + + GSM2801896: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560987 + GSM2801896 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801896 + + + + + + + GEO Accession + GSM2801896 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560987 + SAMN07730048 + GSM2801896 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560987 + SAMN07730048 + GSM2801896 + + + + + + + SRR6124610 + GSM2801896_r1 + + + + + + SRS2560987 + SAMN07730048 + GSM2801896 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237262 + + GSM2801895: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560986 + GSM2801895 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801895 + + + + + + + GEO Accession + GSM2801895 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560986 + SAMN07730049 + GSM2801895 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560986 + SAMN07730049 + GSM2801895 + + + + + + + SRR6124609 + GSM2801895_r1 + + + + + + SRS2560986 + SAMN07730049 + GSM2801895 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237261 + + GSM2801894: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560985 + GSM2801894 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801894 + + + + + + + GEO Accession + GSM2801894 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560985 + SAMN07730050 + GSM2801894 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560985 + SAMN07730050 + GSM2801894 + + + + + + + SRR6124608 + GSM2801894_r1 + + + + + + SRS2560985 + SAMN07730050 + GSM2801894 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237260 + + GSM2801893: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560984 + GSM2801893 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801893 + + + + + + + GEO Accession + GSM2801893 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560984 + SAMN07730051 + GSM2801893 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560984 + SAMN07730051 + GSM2801893 + + + + + + + SRR6124607 + GSM2801893_r1 + + + + + + SRS2560984 + SAMN07730051 + GSM2801893 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237259 + + GSM2801892: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560983 + GSM2801892 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801892 + + + + + + + GEO Accession + GSM2801892 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560983 + SAMN07730052 + GSM2801892 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560983 + SAMN07730052 + GSM2801892 + + + + + + + SRR6124606 + GSM2801892_r1 + + + + + + SRS2560983 + SAMN07730052 + GSM2801892 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237258 + + GSM2801891: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560982 + GSM2801891 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801891 + + + + + + + GEO Accession + GSM2801891 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560982 + SAMN07730053 + GSM2801891 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560982 + SAMN07730053 + GSM2801891 + + + + + + + SRR6124605 + GSM2801891_r1 + + + + + + SRS2560982 + SAMN07730053 + GSM2801891 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237257 + + GSM2801890: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560981 + GSM2801890 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801890 + + + + + + + GEO Accession + GSM2801890 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560981 + SAMN07730054 + GSM2801890 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560981 + SAMN07730054 + GSM2801890 + + + + + + + SRR6124604 + GSM2801890_r1 + + + + + + SRS2560981 + SAMN07730054 + GSM2801890 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237256 + + GSM2801889: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560980 + GSM2801889 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801889 + + + + + + + GEO Accession + GSM2801889 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560980 + SAMN07730055 + GSM2801889 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560980 + SAMN07730055 + GSM2801889 + + + + + + + SRR6124603 + GSM2801889_r1 + + + + + + SRS2560980 + SAMN07730055 + GSM2801889 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237255 + + GSM2801888: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560979 + GSM2801888 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801888 + + + + + + + GEO Accession + GSM2801888 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560979 + SAMN07730056 + GSM2801888 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560979 + SAMN07730056 + GSM2801888 + + + + + + + SRR6124602 + GSM2801888_r1 + + + + + + SRS2560979 + SAMN07730056 + GSM2801888 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237254 + + GSM2801887: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560978 + GSM2801887 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801887 + + + + + + + GEO Accession + GSM2801887 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560978 + SAMN07730057 + GSM2801887 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560978 + SAMN07730057 + GSM2801887 + + + + + + + SRR6124601 + GSM2801887_r1 + + + + + + SRS2560978 + SAMN07730057 + GSM2801887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237253 + + GSM2801886: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2561071 + GSM2801886 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801886 + + + + + + + GEO Accession + GSM2801886 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561071 + SAMN07730058 + GSM2801886 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2561071 + SAMN07730058 + GSM2801886 + + + + + + + SRR6124600 + GSM2801886_r1 + + + + + + SRS2561071 + SAMN07730058 + GSM2801886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237252 + + GSM2801885: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560977 + GSM2801885 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801885 + + + + + + + GEO Accession + GSM2801885 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560977 + SAMN07730059 + GSM2801885 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560977 + SAMN07730059 + GSM2801885 + + + + + + + SRR6124599 + GSM2801885_r1 + + + + + + SRS2560977 + SAMN07730059 + GSM2801885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237251 + + GSM2801884: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560976 + GSM2801884 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801884 + + + + + + + GEO Accession + GSM2801884 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560976 + SAMN07730065 + GSM2801884 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560976 + SAMN07730065 + GSM2801884 + + + + + + + SRR6124598 + GSM2801884_r1 + + + + + + SRS2560976 + SAMN07730065 + GSM2801884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237250 + + GSM2801883: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560975 + GSM2801883 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801883 + + + + + + + GEO Accession + GSM2801883 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560975 + SAMN07730066 + GSM2801883 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560975 + SAMN07730066 + GSM2801883 + + + + + + + SRR6124597 + GSM2801883_r1 + + + + + + SRS2560975 + SAMN07730066 + GSM2801883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237249 + + GSM2801882: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560974 + GSM2801882 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801882 + + + + + + + GEO Accession + GSM2801882 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560974 + SAMN07730067 + GSM2801882 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560974 + SAMN07730067 + GSM2801882 + + + + + + + SRR6124596 + GSM2801882_r1 + + + + + + SRS2560974 + SAMN07730067 + GSM2801882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237248 + + GSM2801881: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560973 + GSM2801881 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801881 + + + + + + + GEO Accession + GSM2801881 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560973 + SAMN07730060 + GSM2801881 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560973 + SAMN07730060 + GSM2801881 + + + + + + + SRR6124595 + GSM2801881_r1 + + + + + + SRS2560973 + SAMN07730060 + GSM2801881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237247 + + GSM2801880: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560972 + GSM2801880 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801880 + + + + + + + GEO Accession + GSM2801880 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560972 + SAMN07730061 + GSM2801880 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560972 + SAMN07730061 + GSM2801880 + + + + + + + SRR6124594 + GSM2801880_r1 + + + + + + SRS2560972 + SAMN07730061 + GSM2801880 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237246 + + GSM2801879: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560970 + GSM2801879 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801879 + + + + + + + GEO Accession + GSM2801879 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560970 + SAMN07730062 + GSM2801879 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560970 + SAMN07730062 + GSM2801879 + + + + + + + SRR6124593 + GSM2801879_r1 + + + + + + SRS2560970 + SAMN07730062 + GSM2801879 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237245 + + GSM2801878: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560969 + GSM2801878 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801878 + + + + + + + GEO Accession + GSM2801878 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560969 + SAMN07730063 + GSM2801878 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560969 + SAMN07730063 + GSM2801878 + + + + + + + SRR6124592 + GSM2801878_r1 + + + + + + SRS2560969 + SAMN07730063 + GSM2801878 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237244 + + GSM2801877: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560968 + GSM2801877 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801877 + + + + + + + GEO Accession + GSM2801877 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560968 + SAMN07730064 + GSM2801877 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560968 + SAMN07730064 + GSM2801877 + + + + + + + SRR6124591 + GSM2801877_r1 + + + + + + SRS2560968 + SAMN07730064 + GSM2801877 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237243 + + GSM2801876: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560967 + GSM2801876 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801876 + + + + + + + GEO Accession + GSM2801876 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560967 + SAMN07730068 + GSM2801876 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560967 + SAMN07730068 + GSM2801876 + + + + + + + SRR6124590 + GSM2801876_r1 + + + + + + SRS2560967 + SAMN07730068 + GSM2801876 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237242 + + GSM2801875: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560966 + GSM2801875 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801875 + + + + + + + GEO Accession + GSM2801875 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560966 + SAMN07730069 + GSM2801875 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560966 + SAMN07730069 + GSM2801875 + + + + + + + SRR6124589 + GSM2801875_r1 + + + + + + SRS2560966 + SAMN07730069 + GSM2801875 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237241 + + GSM2801874: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560965 + GSM2801874 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801874 + + + + + + + GEO Accession + GSM2801874 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560965 + SAMN07730070 + GSM2801874 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560965 + SAMN07730070 + GSM2801874 + + + + + + + SRR6124588 + GSM2801874_r1 + + + + + + SRS2560965 + SAMN07730070 + GSM2801874 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237240 + + GSM2801873: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560964 + GSM2801873 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801873 + + + + + + + GEO Accession + GSM2801873 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560964 + SAMN07730071 + GSM2801873 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560964 + SAMN07730071 + GSM2801873 + + + + + + + SRR6124587 + GSM2801873_r1 + + + + + + SRS2560964 + SAMN07730071 + GSM2801873 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237239 + + GSM2801872: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560962 + GSM2801872 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801872 + + + + + + + GEO Accession + GSM2801872 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560962 + SAMN07730072 + GSM2801872 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560962 + SAMN07730072 + GSM2801872 + + + + + + + SRR6124586 + GSM2801872_r1 + + + + + + SRS2560962 + SAMN07730072 + GSM2801872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237238 + + GSM2801871: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a9; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560963 + GSM2801871 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801871 + + + + + + + GEO Accession + GSM2801871 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560963 + SAMN07730073 + GSM2801871 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560963 + SAMN07730073 + GSM2801871 + + + + + + + SRR6124585 + GSM2801871_r1 + + + + + + SRS2560963 + SAMN07730073 + GSM2801871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237237 + + GSM2801870: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a8; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560959 + GSM2801870 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801870 + + + + + + + GEO Accession + GSM2801870 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560959 + SAMN07730074 + GSM2801870 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560959 + SAMN07730074 + GSM2801870 + + + + + + + SRR6124584 + GSM2801870_r1 + + + + + + SRS2560959 + SAMN07730074 + GSM2801870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237236 + + GSM2801869: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a7; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560961 + GSM2801869 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801869 + + + + + + + GEO Accession + GSM2801869 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560961 + SAMN07730075 + GSM2801869 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560961 + SAMN07730075 + GSM2801869 + + + + + + + SRR6124583 + GSM2801869_r1 + + + + + + SRS2560961 + SAMN07730075 + GSM2801869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237235 + + GSM2801868: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a6; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560960 + GSM2801868 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801868 + + + + + + + GEO Accession + GSM2801868 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560960 + SAMN07730083 + GSM2801868 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560960 + SAMN07730083 + GSM2801868 + + + + + + + SRR6124582 + GSM2801868_r1 + + + + + + SRS2560960 + SAMN07730083 + GSM2801868 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237234 + + GSM2801867: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a5; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560958 + GSM2801867 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801867 + + + + + + + GEO Accession + GSM2801867 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560958 + SAMN07730084 + GSM2801867 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560958 + SAMN07730084 + GSM2801867 + + + + + + + SRR6124581 + GSM2801867_r1 + + + + + + SRS2560958 + SAMN07730084 + GSM2801867 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237233 + + GSM2801866: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a4; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560957 + GSM2801866 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801866 + + + + + + + GEO Accession + GSM2801866 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560957 + SAMN07730085 + GSM2801866 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560957 + SAMN07730085 + GSM2801866 + + + + + + + SRR6124580 + GSM2801866_r1 + + + + + + SRS2560957 + SAMN07730085 + GSM2801866 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237232 + + GSM2801865: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a3; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560956 + GSM2801865 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801865 + + + + + + + GEO Accession + GSM2801865 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560956 + SAMN07730086 + GSM2801865 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560956 + SAMN07730086 + GSM2801865 + + + + + + + SRR6124579 + GSM2801865_r1 + + + + + + SRS2560956 + SAMN07730086 + GSM2801865 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237231 + + GSM2801864: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a2; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560954 + GSM2801864 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801864 + + + + + + + GEO Accession + GSM2801864 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560954 + SAMN07730087 + GSM2801864 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560954 + SAMN07730087 + GSM2801864 + + + + + + + SRR6124578 + GSM2801864_r1 + + + + + + SRS2560954 + SAMN07730087 + GSM2801864 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237230 + + GSM2801863: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a12; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560955 + GSM2801863 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801863 + + + + + + + GEO Accession + GSM2801863 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560955 + SAMN07730088 + GSM2801863 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560955 + SAMN07730088 + GSM2801863 + + + + + + + SRR6124577 + GSM2801863_r1 + + + + + + SRS2560955 + SAMN07730088 + GSM2801863 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237229 + + GSM2801862: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a11; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560953 + GSM2801862 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801862 + + + + + + + GEO Accession + GSM2801862 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560953 + SAMN07730089 + GSM2801862 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560953 + SAMN07730089 + GSM2801862 + + + + + + + SRR6124576 + GSM2801862_r1 + + + + + + SRS2560953 + SAMN07730089 + GSM2801862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237228 + + GSM2801861: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a10; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560952 + GSM2801861 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801861 + + + + + + + GEO Accession + GSM2801861 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560952 + SAMN07730090 + GSM2801861 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560952 + SAMN07730090 + GSM2801861 + + + + + + + SRR6124575 + GSM2801861_r1 + + + + + + SRS2560952 + SAMN07730090 + GSM2801861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237227 + + GSM2801860: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a1; Homo sapiens; Mus musculus; RNA-Seq + + + SRP119249 + + + + + + + SRS2560951 + GSM2801860 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801860 + + + + + + + GEO Accession + GSM2801860 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560951 + SAMN07730091 + GSM2801860 + + U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from U87-3T3 cell mixture + + + cell line + U87 and 3T3 + + + + + + + SRS2560951 + SAMN07730091 + GSM2801860 + + + + + + + SRR6124574 + GSM2801860_r1 + + + + + + SRS2560951 + SAMN07730091 + GSM2801860 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237226 + + GSM2801859: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560950 + GSM2801859 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801859 + + + + + + + GEO Accession + GSM2801859 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560950 + SAMN07730092 + GSM2801859 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560950 + SAMN07730092 + GSM2801859 + + + + + + + SRR6124573 + GSM2801859_r1 + + + + + + SRS2560950 + SAMN07730092 + GSM2801859 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237225 + + GSM2801858: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560949 + GSM2801858 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801858 + + + + + + + GEO Accession + GSM2801858 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560949 + SAMN07730093 + GSM2801858 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560949 + SAMN07730093 + GSM2801858 + + + + + + + SRR6124572 + GSM2801858_r1 + + + + + + SRS2560949 + SAMN07730093 + GSM2801858 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237224 + + GSM2801857: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560948 + GSM2801857 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801857 + + + + + + + GEO Accession + GSM2801857 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560948 + SAMN07730094 + GSM2801857 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560948 + SAMN07730094 + GSM2801857 + + + + + + + SRR6124571 + GSM2801857_r1 + + + + + + SRS2560948 + SAMN07730094 + GSM2801857 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237223 + + GSM2801856: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560947 + GSM2801856 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801856 + + + + + + + GEO Accession + GSM2801856 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560947 + SAMN07730095 + GSM2801856 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560947 + SAMN07730095 + GSM2801856 + + + + + + + SRR6124570 + GSM2801856_r1 + + + + + + SRS2560947 + SAMN07730095 + GSM2801856 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237222 + + GSM2801855: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560946 + GSM2801855 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801855 + + + + + + + GEO Accession + GSM2801855 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560946 + SAMN07730096 + GSM2801855 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560946 + SAMN07730096 + GSM2801855 + + + + + + + SRR6124569 + GSM2801855_r1 + + + + + + SRS2560946 + SAMN07730096 + GSM2801855 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237221 + + GSM2801854: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560944 + GSM2801854 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801854 + + + + + + + GEO Accession + GSM2801854 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560944 + SAMN07730097 + GSM2801854 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560944 + SAMN07730097 + GSM2801854 + + + + + + + SRR6124568 + GSM2801854_r1 + + + + + + SRS2560944 + SAMN07730097 + GSM2801854 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237220 + + GSM2801853: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560943 + GSM2801853 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801853 + + + + + + + GEO Accession + GSM2801853 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560943 + SAMN07730098 + GSM2801853 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560943 + SAMN07730098 + GSM2801853 + + + + + + + SRR6124567 + GSM2801853_r1 + + + + + + SRS2560943 + SAMN07730098 + GSM2801853 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237219 + + GSM2801852: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560942 + GSM2801852 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801852 + + + + + + + GEO Accession + GSM2801852 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560942 + SAMN07730099 + GSM2801852 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560942 + SAMN07730099 + GSM2801852 + + + + + + + SRR6124566 + GSM2801852_r1 + + + + + + SRS2560942 + SAMN07730099 + GSM2801852 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237218 + + GSM2801851: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560941 + GSM2801851 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801851 + + + + + + + GEO Accession + GSM2801851 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560941 + SAMN07730100 + GSM2801851 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560941 + SAMN07730100 + GSM2801851 + + + + + + + SRR6124565 + GSM2801851_r1 + + + + + + SRS2560941 + SAMN07730100 + GSM2801851 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237217 + + GSM2801850: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560940 + GSM2801850 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801850 + + + + + + + GEO Accession + GSM2801850 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560940 + SAMN07730101 + GSM2801850 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560940 + SAMN07730101 + GSM2801850 + + + + + + + SRR6124564 + GSM2801850_r1 + + + + + + SRS2560940 + SAMN07730101 + GSM2801850 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237216 + + GSM2801849: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560939 + GSM2801849 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801849 + + + + + + + GEO Accession + GSM2801849 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560939 + SAMN07730102 + GSM2801849 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560939 + SAMN07730102 + GSM2801849 + + + + + + + SRR6124563 + GSM2801849_r1 + + + + + + SRS2560939 + SAMN07730102 + GSM2801849 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237215 + + GSM2801848: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560938 + GSM2801848 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801848 + + + + + + + GEO Accession + GSM2801848 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560938 + SAMN07730103 + GSM2801848 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560938 + SAMN07730103 + GSM2801848 + + + + + + + SRR6124562 + GSM2801848_r1 + + + + + + SRS2560938 + SAMN07730103 + GSM2801848 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237214 + + GSM2801847: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560937 + GSM2801847 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801847 + + + + + + + GEO Accession + GSM2801847 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560937 + SAMN07730104 + GSM2801847 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560937 + SAMN07730104 + GSM2801847 + + + + + + + SRR6124561 + GSM2801847_r1 + + + + + + SRS2560937 + SAMN07730104 + GSM2801847 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237213 + + GSM2801846: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560935 + GSM2801846 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801846 + + + + + + + GEO Accession + GSM2801846 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560935 + SAMN07730105 + GSM2801846 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560935 + SAMN07730105 + GSM2801846 + + + + + + + SRR6124560 + GSM2801846_r1 + + + + + + SRS2560935 + SAMN07730105 + GSM2801846 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237212 + + GSM2801845: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560934 + GSM2801845 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801845 + + + + + + + GEO Accession + GSM2801845 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560934 + SAMN07730106 + GSM2801845 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560934 + SAMN07730106 + GSM2801845 + + + + + + + SRR6124559 + GSM2801845_r1 + + + + + + SRS2560934 + SAMN07730106 + GSM2801845 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237211 + + GSM2801844: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560933 + GSM2801844 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801844 + + + + + + + GEO Accession + GSM2801844 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560933 + SAMN07730107 + GSM2801844 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560933 + SAMN07730107 + GSM2801844 + + + + + + + SRR6124558 + GSM2801844_r1 + + + + + + SRS2560933 + SAMN07730107 + GSM2801844 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237210 + + GSM2801843: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560932 + GSM2801843 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801843 + + + + + + + GEO Accession + GSM2801843 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560932 + SAMN07730108 + GSM2801843 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560932 + SAMN07730108 + GSM2801843 + + + + + + + SRR6124557 + GSM2801843_r1 + + + + + + SRS2560932 + SAMN07730108 + GSM2801843 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237209 + + GSM2801842: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560931 + GSM2801842 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801842 + + + + + + + GEO Accession + GSM2801842 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560931 + SAMN07730109 + GSM2801842 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560931 + SAMN07730109 + GSM2801842 + + + + + + + SRR6124556 + GSM2801842_r1 + + + + + + SRS2560931 + SAMN07730109 + GSM2801842 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237208 + + GSM2801841: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560930 + GSM2801841 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801841 + + + + + + + GEO Accession + GSM2801841 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560930 + SAMN07730110 + GSM2801841 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560930 + SAMN07730110 + GSM2801841 + + + + + + + SRR6124555 + GSM2801841_r1 + + + + + + SRS2560930 + SAMN07730110 + GSM2801841 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237207 + + GSM2801840: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2561002 + GSM2801840 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801840 + + + + + + + GEO Accession + GSM2801840 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2561002 + SAMN07730111 + GSM2801840 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2561002 + SAMN07730111 + GSM2801840 + + + + + + + SRR6124554 + GSM2801840_r1 + + + + + + SRS2561002 + SAMN07730111 + GSM2801840 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237206 + + GSM2801839: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560929 + GSM2801839 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801839 + + + + + + + GEO Accession + GSM2801839 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560929 + SAMN07730112 + GSM2801839 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560929 + SAMN07730112 + GSM2801839 + + + + + + + SRR6124553 + GSM2801839_r1 + + + + + + SRS2560929 + SAMN07730112 + GSM2801839 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237205 + + GSM2801838: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560928 + GSM2801838 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801838 + + + + + + + GEO Accession + GSM2801838 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560928 + SAMN07730113 + GSM2801838 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560928 + SAMN07730113 + GSM2801838 + + + + + + + SRR6124552 + GSM2801838_r1 + + + + + + SRS2560928 + SAMN07730113 + GSM2801838 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237204 + + GSM2801837: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560927 + GSM2801837 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801837 + + + + + + + GEO Accession + GSM2801837 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560927 + SAMN07730114 + GSM2801837 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560927 + SAMN07730114 + GSM2801837 + + + + + + + SRR6124551 + GSM2801837_r1 + + + + + + SRS2560927 + SAMN07730114 + GSM2801837 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237203 + + GSM2801836: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560926 + GSM2801836 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801836 + + + + + + + GEO Accession + GSM2801836 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560926 + SAMN07730115 + GSM2801836 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560926 + SAMN07730115 + GSM2801836 + + + + + + + SRR6124550 + GSM2801836_r1 + + + + + + SRS2560926 + SAMN07730115 + GSM2801836 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237202 + + GSM2801835: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560989 + GSM2801835 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801835 + + + + + + + GEO Accession + GSM2801835 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560989 + SAMN07730116 + GSM2801835 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560989 + SAMN07730116 + GSM2801835 + + + + + + + SRR6124549 + GSM2801835_r1 + + + + + + SRS2560989 + SAMN07730116 + GSM2801835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237201 + + GSM2801834: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560924 + GSM2801834 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801834 + + + + + + + GEO Accession + GSM2801834 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560924 + SAMN07730117 + GSM2801834 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560924 + SAMN07730117 + GSM2801834 + + + + + + + SRR6124548 + GSM2801834_r1 + + + + + + SRS2560924 + SAMN07730117 + GSM2801834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237200 + + GSM2801833: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560925 + GSM2801833 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801833 + + + + + + + GEO Accession + GSM2801833 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560925 + SAMN07730118 + GSM2801833 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560925 + SAMN07730118 + GSM2801833 + + + + + + + SRR6124547 + GSM2801833_r1 + + + + + + SRS2560925 + SAMN07730118 + GSM2801833 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237199 + + GSM2801832: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560923 + GSM2801832 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801832 + + + + + + + GEO Accession + GSM2801832 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560923 + SAMN07730119 + GSM2801832 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560923 + SAMN07730119 + GSM2801832 + + + + + + + SRR6124546 + GSM2801832_r1 + + + + + + SRS2560923 + SAMN07730119 + GSM2801832 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237198 + + GSM2801831: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560922 + GSM2801831 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801831 + + + + + + + GEO Accession + GSM2801831 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560922 + SAMN07730120 + GSM2801831 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560922 + SAMN07730120 + GSM2801831 + + + + + + + SRR6124545 + GSM2801831_r1 + + + + + + SRS2560922 + SAMN07730120 + GSM2801831 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237197 + + GSM2801830: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560921 + GSM2801830 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801830 + + + + + + + GEO Accession + GSM2801830 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560921 + SAMN07730121 + GSM2801830 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560921 + SAMN07730121 + GSM2801830 + + + + + + + SRR6124544 + GSM2801830_r1 + + + + + + SRS2560921 + SAMN07730121 + GSM2801830 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237196 + + GSM2801829: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560920 + GSM2801829 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801829 + + + + + + + GEO Accession + GSM2801829 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560920 + SAMN07730122 + GSM2801829 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560920 + SAMN07730122 + GSM2801829 + + + + + + + SRR6124543 + GSM2801829_r1 + + + + + + SRS2560920 + SAMN07730122 + GSM2801829 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237195 + + GSM2801828: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560919 + GSM2801828 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801828 + + + + + + + GEO Accession + GSM2801828 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560919 + SAMN07730123 + GSM2801828 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560919 + SAMN07730123 + GSM2801828 + + + + + + + SRR6124542 + GSM2801828_r1 + + + + + + SRS2560919 + SAMN07730123 + GSM2801828 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237194 + + GSM2801827: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560918 + GSM2801827 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801827 + + + + + + + GEO Accession + GSM2801827 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560918 + SAMN07730124 + GSM2801827 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560918 + SAMN07730124 + GSM2801827 + + + + + + + SRR6124541 + GSM2801827_r1 + + + + + + SRS2560918 + SAMN07730124 + GSM2801827 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237193 + + GSM2801826: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560917 + GSM2801826 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801826 + + + + + + + GEO Accession + GSM2801826 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560917 + SAMN07730125 + GSM2801826 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560917 + SAMN07730125 + GSM2801826 + + + + + + + SRR6124540 + GSM2801826_r1 + + + + + + SRS2560917 + SAMN07730125 + GSM2801826 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237192 + + GSM2801825: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560916 + GSM2801825 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801825 + + + + + + + GEO Accession + GSM2801825 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560916 + SAMN07730126 + GSM2801825 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560916 + SAMN07730126 + GSM2801825 + + + + + + + SRR6124539 + GSM2801825_r1 + + + + + + SRS2560916 + SAMN07730126 + GSM2801825 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237191 + + GSM2801824: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560915 + GSM2801824 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801824 + + + + + + + GEO Accession + GSM2801824 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560915 + SAMN07730127 + GSM2801824 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560915 + SAMN07730127 + GSM2801824 + + + + + + + SRR6124538 + GSM2801824_r1 + + + + + + SRS2560915 + SAMN07730127 + GSM2801824 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237190 + + GSM2801823: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560914 + GSM2801823 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801823 + + + + + + + GEO Accession + GSM2801823 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560914 + SAMN07730128 + GSM2801823 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560914 + SAMN07730128 + GSM2801823 + + + + + + + SRR6124537 + GSM2801823_r1 + + + + + + SRS2560914 + SAMN07730128 + GSM2801823 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237189 + + GSM2801822: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560913 + GSM2801822 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801822 + + + + + + + GEO Accession + GSM2801822 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560913 + SAMN07730129 + GSM2801822 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560913 + SAMN07730129 + GSM2801822 + + + + + + + SRR6124536 + GSM2801822_r1 + + + + + + SRS2560913 + SAMN07730129 + GSM2801822 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237188 + + GSM2801821: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560912 + GSM2801821 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801821 + + + + + + + GEO Accession + GSM2801821 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560912 + SAMN07730130 + GSM2801821 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560912 + SAMN07730130 + GSM2801821 + + + + + + + SRR6124535 + GSM2801821_r1 + + + + + + SRS2560912 + SAMN07730130 + GSM2801821 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237187 + + GSM2801820: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560911 + GSM2801820 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801820 + + + + + + + GEO Accession + GSM2801820 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560911 + SAMN07730131 + GSM2801820 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560911 + SAMN07730131 + GSM2801820 + + + + + + + SRR6124534 + GSM2801820_r1 + + + + + + SRS2560911 + SAMN07730131 + GSM2801820 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237186 + + GSM2801819: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560910 + GSM2801819 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801819 + + + + + + + GEO Accession + GSM2801819 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560910 + SAMN07730132 + GSM2801819 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560910 + SAMN07730132 + GSM2801819 + + + + + + + SRR6124533 + GSM2801819_r1 + + + + + + SRS2560910 + SAMN07730132 + GSM2801819 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237185 + + GSM2801818: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560909 + GSM2801818 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801818 + + + + + + + GEO Accession + GSM2801818 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560909 + SAMN07730133 + GSM2801818 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560909 + SAMN07730133 + GSM2801818 + + + + + + + SRR6124532 + GSM2801818_r1 + + + + + + SRS2560909 + SAMN07730133 + GSM2801818 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237184 + + GSM2801817: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560908 + GSM2801817 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801817 + + + + + + + GEO Accession + GSM2801817 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560908 + SAMN07730134 + GSM2801817 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560908 + SAMN07730134 + GSM2801817 + + + + + + + SRR6124531 + GSM2801817_r1 + + + + + + SRS2560908 + SAMN07730134 + GSM2801817 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237183 + + GSM2801816: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560907 + GSM2801816 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801816 + + + + + + + GEO Accession + GSM2801816 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560907 + SAMN07730135 + GSM2801816 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560907 + SAMN07730135 + GSM2801816 + + + + + + + SRR6124530 + GSM2801816_r1 + + + + + + SRS2560907 + SAMN07730135 + GSM2801816 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237182 + + GSM2801815: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560906 + GSM2801815 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801815 + + + + + + + GEO Accession + GSM2801815 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560906 + SAMN07730136 + GSM2801815 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560906 + SAMN07730136 + GSM2801815 + + + + + + + SRR6124529 + GSM2801815_r1 + + + + + + SRS2560906 + SAMN07730136 + GSM2801815 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237181 + + GSM2801814: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560971 + GSM2801814 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801814 + + + + + + + GEO Accession + GSM2801814 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560971 + SAMN07730137 + GSM2801814 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560971 + SAMN07730137 + GSM2801814 + + + + + + + SRR6124528 + GSM2801814_r1 + + + + + + SRS2560971 + SAMN07730137 + GSM2801814 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237180 + + GSM2801813: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560903 + GSM2801813 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801813 + + + + + + + GEO Accession + GSM2801813 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560903 + SAMN07730138 + GSM2801813 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560903 + SAMN07730138 + GSM2801813 + + + + + + + SRR6124527 + GSM2801813_r1 + + + + + + SRS2560903 + SAMN07730138 + GSM2801813 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237179 + + GSM2801812: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560905 + GSM2801812 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801812 + + + + + + + GEO Accession + GSM2801812 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560905 + SAMN07730139 + GSM2801812 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560905 + SAMN07730139 + GSM2801812 + + + + + + + SRR6124526 + GSM2801812_r1 + + + + + + SRS2560905 + SAMN07730139 + GSM2801812 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237178 + + GSM2801811: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560904 + GSM2801811 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801811 + + + + + + + GEO Accession + GSM2801811 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560904 + SAMN07730140 + GSM2801811 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560904 + SAMN07730140 + GSM2801811 + + + + + + + SRR6124525 + GSM2801811_r1 + + + + + + SRS2560904 + SAMN07730140 + GSM2801811 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237177 + + GSM2801810: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560902 + GSM2801810 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801810 + + + + + + + GEO Accession + GSM2801810 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560902 + SAMN07730141 + GSM2801810 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560902 + SAMN07730141 + GSM2801810 + + + + + + + SRR6124524 + GSM2801810_r1 + + + + + + SRS2560902 + SAMN07730141 + GSM2801810 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237176 + + GSM2801809: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560899 + GSM2801809 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801809 + + + + + + + GEO Accession + GSM2801809 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560899 + SAMN07730142 + GSM2801809 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560899 + SAMN07730142 + GSM2801809 + + + + + + + SRR6124523 + GSM2801809_r1 + + + + + + SRS2560899 + SAMN07730142 + GSM2801809 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237175 + + GSM2801808: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560901 + GSM2801808 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801808 + + + + + + + GEO Accession + GSM2801808 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560901 + SAMN07730143 + GSM2801808 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560901 + SAMN07730143 + GSM2801808 + + + + + + + SRR6124522 + GSM2801808_r1 + + + + + + SRS2560901 + SAMN07730143 + GSM2801808 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237174 + + GSM2801807: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560900 + GSM2801807 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801807 + + + + + + + GEO Accession + GSM2801807 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560900 + SAMN07730144 + GSM2801807 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560900 + SAMN07730144 + GSM2801807 + + + + + + + SRR6124521 + GSM2801807_r1 + + + + + + SRS2560900 + SAMN07730144 + GSM2801807 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237173 + + GSM2801806: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560898 + GSM2801806 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801806 + + + + + + + GEO Accession + GSM2801806 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560898 + SAMN07730145 + GSM2801806 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560898 + SAMN07730145 + GSM2801806 + + + + + + + SRR6124520 + GSM2801806_r1 + + + + + + SRS2560898 + SAMN07730145 + GSM2801806 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237172 + + GSM2801805: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560895 + GSM2801805 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801805 + + + + + + + GEO Accession + GSM2801805 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560895 + SAMN07730146 + GSM2801805 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560895 + SAMN07730146 + GSM2801805 + + + + + + + SRR6124519 + GSM2801805_r1 + + + + + + SRS2560895 + SAMN07730146 + GSM2801805 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237171 + + GSM2801804: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560897 + GSM2801804 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801804 + + + + + + + GEO Accession + GSM2801804 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560897 + SAMN07729890 + GSM2801804 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560897 + SAMN07729890 + GSM2801804 + + + + + + + SRR6124518 + GSM2801804_r1 + + + + + + SRS2560897 + SAMN07729890 + GSM2801804 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237170 + + GSM2801803: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560896 + GSM2801803 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801803 + + + + + + + GEO Accession + GSM2801803 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560896 + SAMN07729891 + GSM2801803 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560896 + SAMN07729891 + GSM2801803 + + + + + + + SRR6124517 + GSM2801803_r1 + + + + + + SRS2560896 + SAMN07729891 + GSM2801803 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237169 + + GSM2801802: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560894 + GSM2801802 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801802 + + + + + + + GEO Accession + GSM2801802 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560894 + SAMN07729892 + GSM2801802 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560894 + SAMN07729892 + GSM2801802 + + + + + + + SRR6124516 + GSM2801802_r1 + + + + + + SRS2560894 + SAMN07729892 + GSM2801802 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237168 + + GSM2801801: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560892 + GSM2801801 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801801 + + + + + + + GEO Accession + GSM2801801 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560892 + SAMN07729893 + GSM2801801 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560892 + SAMN07729893 + GSM2801801 + + + + + + + SRR6124515 + GSM2801801_r1 + + + + + + SRS2560892 + SAMN07729893 + GSM2801801 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237167 + + GSM2801800: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560891 + GSM2801800 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801800 + + + + + + + GEO Accession + GSM2801800 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560891 + SAMN07729894 + GSM2801800 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560891 + SAMN07729894 + GSM2801800 + + + + + + + SRR6124514 + GSM2801800_r1 + + + + + + SRS2560891 + SAMN07729894 + GSM2801800 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237166 + + GSM2801799: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560893 + GSM2801799 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801799 + + + + + + + GEO Accession + GSM2801799 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560893 + SAMN07729895 + GSM2801799 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560893 + SAMN07729895 + GSM2801799 + + + + + + + SRR6124513 + GSM2801799_r1 + + + + + + SRS2560893 + SAMN07729895 + GSM2801799 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237165 + + GSM2801798: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560890 + GSM2801798 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801798 + + + + + + + GEO Accession + GSM2801798 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560890 + SAMN07729896 + GSM2801798 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560890 + SAMN07729896 + GSM2801798 + + + + + + + SRR6124512 + GSM2801798_r1 + + + + + + SRS2560890 + SAMN07729896 + GSM2801798 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237164 + + GSM2801797: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560889 + GSM2801797 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801797 + + + + + + + GEO Accession + GSM2801797 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560889 + SAMN07729897 + GSM2801797 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560889 + SAMN07729897 + GSM2801797 + + + + + + + SRR6124511 + GSM2801797_r1 + + + + + + SRS2560889 + SAMN07729897 + GSM2801797 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237163 + + GSM2801796: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560888 + GSM2801796 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801796 + + + + + + + GEO Accession + GSM2801796 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560888 + SAMN07729898 + GSM2801796 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560888 + SAMN07729898 + GSM2801796 + + + + + + + SRR6124510 + GSM2801796_r1 + + + + + + SRS2560888 + SAMN07729898 + GSM2801796 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237162 + + GSM2801795: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560887 + GSM2801795 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801795 + + + + + + + GEO Accession + GSM2801795 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560887 + SAMN07729899 + GSM2801795 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560887 + SAMN07729899 + GSM2801795 + + + + + + + SRR6124509 + GSM2801795_r1 + + + + + + SRS2560887 + SAMN07729899 + GSM2801795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237161 + + GSM2801794: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560886 + GSM2801794 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801794 + + + + + + + GEO Accession + GSM2801794 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560886 + SAMN07729900 + GSM2801794 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560886 + SAMN07729900 + GSM2801794 + + + + + + + SRR6124508 + GSM2801794_r1 + + + + + + SRS2560886 + SAMN07729900 + GSM2801794 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237160 + + GSM2801793: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560885 + GSM2801793 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801793 + + + + + + + GEO Accession + GSM2801793 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560885 + SAMN07729901 + GSM2801793 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560885 + SAMN07729901 + GSM2801793 + + + + + + + SRR6124507 + GSM2801793_r1 + + + + + + SRS2560885 + SAMN07729901 + GSM2801793 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237159 + + GSM2801792: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560884 + GSM2801792 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801792 + + + + + + + GEO Accession + GSM2801792 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560884 + SAMN07729902 + GSM2801792 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560884 + SAMN07729902 + GSM2801792 + + + + + + + SRR6124506 + GSM2801792_r1 + + + + + + SRS2560884 + SAMN07729902 + GSM2801792 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237158 + + GSM2801791: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560883 + GSM2801791 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801791 + + + + + + + GEO Accession + GSM2801791 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560883 + SAMN07729903 + GSM2801791 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560883 + SAMN07729903 + GSM2801791 + + + + + + + SRR6124505 + GSM2801791_r1 + + + + + + SRS2560883 + SAMN07729903 + GSM2801791 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237157 + + GSM2801790: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560882 + GSM2801790 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801790 + + + + + + + GEO Accession + GSM2801790 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560882 + SAMN07729904 + GSM2801790 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560882 + SAMN07729904 + GSM2801790 + + + + + + + SRR6124504 + GSM2801790_r1 + + + + + + SRS2560882 + SAMN07729904 + GSM2801790 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237156 + + GSM2801789: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560881 + GSM2801789 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801789 + + + + + + + GEO Accession + GSM2801789 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560881 + SAMN07729905 + GSM2801789 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560881 + SAMN07729905 + GSM2801789 + + + + + + + SRR6124503 + GSM2801789_r1 + + + + + + SRS2560881 + SAMN07729905 + GSM2801789 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237155 + + GSM2801788: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560880 + GSM2801788 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801788 + + + + + + + GEO Accession + GSM2801788 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560880 + SAMN07730184 + GSM2801788 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560880 + SAMN07730184 + GSM2801788 + + + + + + + SRR6124502 + GSM2801788_r1 + + + + + + SRS2560880 + SAMN07730184 + GSM2801788 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237154 + + GSM2801787: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560878 + GSM2801787 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801787 + + + + + + + GEO Accession + GSM2801787 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560878 + SAMN07730185 + GSM2801787 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560878 + SAMN07730185 + GSM2801787 + + + + + + + SRR6124501 + GSM2801787_r1 + + + + + + SRS2560878 + SAMN07730185 + GSM2801787 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237153 + + GSM2801786: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560879 + GSM2801786 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801786 + + + + + + + GEO Accession + GSM2801786 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560879 + SAMN07730186 + GSM2801786 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560879 + SAMN07730186 + GSM2801786 + + + + + + + SRR6124500 + GSM2801786_r1 + + + + + + SRS2560879 + SAMN07730186 + GSM2801786 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237152 + + GSM2801785: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560877 + GSM2801785 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801785 + + + + + + + GEO Accession + GSM2801785 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560877 + SAMN07730187 + GSM2801785 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560877 + SAMN07730187 + GSM2801785 + + + + + + + SRR6124499 + GSM2801785_r1 + + + + + + SRS2560877 + SAMN07730187 + GSM2801785 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237151 + + GSM2801784: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560876 + GSM2801784 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801784 + + + + + + + GEO Accession + GSM2801784 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560876 + SAMN07730188 + GSM2801784 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560876 + SAMN07730188 + GSM2801784 + + + + + + + SRR6124498 + GSM2801784_r1 + + + + + + SRS2560876 + SAMN07730188 + GSM2801784 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237150 + + GSM2801783: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560875 + GSM2801783 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801783 + + + + + + + GEO Accession + GSM2801783 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560875 + SAMN07730189 + GSM2801783 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560875 + SAMN07730189 + GSM2801783 + + + + + + + SRR6124497 + GSM2801783_r1 + + + + + + SRS2560875 + SAMN07730189 + GSM2801783 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237149 + + GSM2801782: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560874 + GSM2801782 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801782 + + + + + + + GEO Accession + GSM2801782 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560874 + SAMN07730190 + GSM2801782 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560874 + SAMN07730190 + GSM2801782 + + + + + + + SRR6124496 + GSM2801782_r1 + + + + + + SRS2560874 + SAMN07730190 + GSM2801782 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237148 + + GSM2801781: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560873 + GSM2801781 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801781 + + + + + + + GEO Accession + GSM2801781 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560873 + SAMN07730191 + GSM2801781 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560873 + SAMN07730191 + GSM2801781 + + + + + + + SRR6124495 + GSM2801781_r1 + + + + + + SRS2560873 + SAMN07730191 + GSM2801781 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237147 + + GSM2801780: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560872 + GSM2801780 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801780 + + + + + + + GEO Accession + GSM2801780 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560872 + SAMN07730192 + GSM2801780 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560872 + SAMN07730192 + GSM2801780 + + + + + + + SRR6124494 + GSM2801780_r1 + + + + + + SRS2560872 + SAMN07730192 + GSM2801780 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237146 + + GSM2801779: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560871 + GSM2801779 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801779 + + + + + + + GEO Accession + GSM2801779 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560871 + SAMN07730193 + GSM2801779 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560871 + SAMN07730193 + GSM2801779 + + + + + + + SRR6124493 + GSM2801779_r1 + + + + + + SRS2560871 + SAMN07730193 + GSM2801779 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237145 + + GSM2801778: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560870 + GSM2801778 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801778 + + + + + + + GEO Accession + GSM2801778 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560870 + SAMN07730194 + GSM2801778 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560870 + SAMN07730194 + GSM2801778 + + + + + + + SRR6124492 + GSM2801778_r1 + + + + + + SRS2560870 + SAMN07730194 + GSM2801778 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237144 + + GSM2801777: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560869 + GSM2801777 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801777 + + + + + + + GEO Accession + GSM2801777 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560869 + SAMN07730195 + GSM2801777 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560869 + SAMN07730195 + GSM2801777 + + + + + + + SRR6124491 + GSM2801777_r1 + + + + + + SRS2560869 + SAMN07730195 + GSM2801777 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237143 + + GSM2801776: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560868 + GSM2801776 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801776 + + + + + + + GEO Accession + GSM2801776 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560868 + SAMN07730196 + GSM2801776 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560868 + SAMN07730196 + GSM2801776 + + + + + + + SRR6124490 + GSM2801776_r1 + + + + + + SRS2560868 + SAMN07730196 + GSM2801776 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237142 + + GSM2801775: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560867 + GSM2801775 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801775 + + + + + + + GEO Accession + GSM2801775 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560867 + SAMN07730197 + GSM2801775 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560867 + SAMN07730197 + GSM2801775 + + + + + + + SRR6124489 + GSM2801775_r1 + + + + + + SRS2560867 + SAMN07730197 + GSM2801775 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237141 + + GSM2801774: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560866 + GSM2801774 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801774 + + + + + + + GEO Accession + GSM2801774 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560866 + SAMN07730198 + GSM2801774 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560866 + SAMN07730198 + GSM2801774 + + + + + + + SRR6124488 + GSM2801774_r1 + + + + + + SRS2560866 + SAMN07730198 + GSM2801774 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237140 + + GSM2801773: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560865 + GSM2801773 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801773 + + + + + + + GEO Accession + GSM2801773 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560865 + SAMN07730199 + GSM2801773 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560865 + SAMN07730199 + GSM2801773 + + + + + + + SRR6124487 + GSM2801773_r1 + + + + + + SRS2560865 + SAMN07730199 + GSM2801773 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237139 + + GSM2801772: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560864 + GSM2801772 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801772 + + + + + + + GEO Accession + GSM2801772 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560864 + SAMN07730200 + GSM2801772 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560864 + SAMN07730200 + GSM2801772 + + + + + + + SRR6124486 + GSM2801772_r1 + + + + + + SRS2560864 + SAMN07730200 + GSM2801772 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237138 + + GSM2801771: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560945 + GSM2801771 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801771 + + + + + + + GEO Accession + GSM2801771 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560945 + SAMN07730201 + GSM2801771 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560945 + SAMN07730201 + GSM2801771 + + + + + + + SRR6124485 + GSM2801771_r1 + + + + + + SRS2560945 + SAMN07730201 + GSM2801771 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237137 + + GSM2801770: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560863 + GSM2801770 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801770 + + + + + + + GEO Accession + GSM2801770 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560863 + SAMN07730202 + GSM2801770 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560863 + SAMN07730202 + GSM2801770 + + + + + + + SRR6124484 + GSM2801770_r1 + + + + + + SRS2560863 + SAMN07730202 + GSM2801770 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237136 + + GSM2801769: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560936 + GSM2801769 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801769 + + + + + + + GEO Accession + GSM2801769 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560936 + SAMN07730203 + GSM2801769 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560936 + SAMN07730203 + GSM2801769 + + + + + + + SRR6124483 + GSM2801769_r1 + + + + + + SRS2560936 + SAMN07730203 + GSM2801769 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237135 + + GSM2801768: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560862 + GSM2801768 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801768 + + + + + + + GEO Accession + GSM2801768 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560862 + SAMN07730204 + GSM2801768 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560862 + SAMN07730204 + GSM2801768 + + + + + + + SRR6124482 + GSM2801768_r1 + + + + + + SRS2560862 + SAMN07730204 + GSM2801768 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237134 + + GSM2801767: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560861 + GSM2801767 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801767 + + + + + + + GEO Accession + GSM2801767 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560861 + SAMN07730205 + GSM2801767 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560861 + SAMN07730205 + GSM2801767 + + + + + + + SRR6124481 + GSM2801767_r1 + + + + + + SRS2560861 + SAMN07730205 + GSM2801767 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237133 + + GSM2801766: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560860 + GSM2801766 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801766 + + + + + + + GEO Accession + GSM2801766 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560860 + SAMN07730206 + GSM2801766 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560860 + SAMN07730206 + GSM2801766 + + + + + + + SRR6124480 + GSM2801766_r1 + + + + + + SRS2560860 + SAMN07730206 + GSM2801766 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237132 + + GSM2801765: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560859 + GSM2801765 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801765 + + + + + + + GEO Accession + GSM2801765 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560859 + SAMN07730207 + GSM2801765 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560859 + SAMN07730207 + GSM2801765 + + + + + + + SRR6124479 + GSM2801765_r1 + + + + + + SRS2560859 + SAMN07730207 + GSM2801765 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237131 + + GSM2801764: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560858 + GSM2801764 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801764 + + + + + + + GEO Accession + GSM2801764 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560858 + SAMN07730208 + GSM2801764 + + HEK293 scRNA-Seq Plate2 HEK293_SC_P2a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560858 + SAMN07730208 + GSM2801764 + + + + + + + SRR6124478 + GSM2801764_r1 + + + + + + SRS2560858 + SAMN07730208 + GSM2801764 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237130 + + GSM2801763: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560857 + GSM2801763 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801763 + + + + + + + GEO Accession + GSM2801763 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560857 + SAMN07729845 + GSM2801763 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560857 + SAMN07729845 + GSM2801763 + + + + + + + SRR6124477 + GSM2801763_r1 + + + + + + SRS2560857 + SAMN07729845 + GSM2801763 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237129 + + GSM2801762: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560856 + GSM2801762 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801762 + + + + + + + GEO Accession + GSM2801762 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560856 + SAMN07729846 + GSM2801762 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560856 + SAMN07729846 + GSM2801762 + + + + + + + SRR6124476 + GSM2801762_r1 + + + + + + SRS2560856 + SAMN07729846 + GSM2801762 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237128 + + GSM2801761: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560855 + GSM2801761 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801761 + + + + + + + GEO Accession + GSM2801761 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560855 + SAMN07730209 + GSM2801761 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560855 + SAMN07730209 + GSM2801761 + + + + + + + SRR6124475 + GSM2801761_r1 + + + + + + SRS2560855 + SAMN07730209 + GSM2801761 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237127 + + GSM2801760: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560854 + GSM2801760 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801760 + + + + + + + GEO Accession + GSM2801760 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560854 + SAMN07730210 + GSM2801760 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560854 + SAMN07730210 + GSM2801760 + + + + + + + SRR6124474 + GSM2801760_r1 + + + + + + SRS2560854 + SAMN07730210 + GSM2801760 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237126 + + GSM2801759: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560853 + GSM2801759 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801759 + + + + + + + GEO Accession + GSM2801759 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560853 + SAMN07730211 + GSM2801759 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560853 + SAMN07730211 + GSM2801759 + + + + + + + SRR6124473 + GSM2801759_r1 + + + + + + SRS2560853 + SAMN07730211 + GSM2801759 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237125 + + GSM2801758: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560851 + GSM2801758 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801758 + + + + + + + GEO Accession + GSM2801758 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560851 + SAMN07730212 + GSM2801758 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560851 + SAMN07730212 + GSM2801758 + + + + + + + SRR6124472 + GSM2801758_r1 + + + + + + SRS2560851 + SAMN07730212 + GSM2801758 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237124 + + GSM2801757: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560850 + GSM2801757 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801757 + + + + + + + GEO Accession + GSM2801757 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560850 + SAMN07730213 + GSM2801757 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560850 + SAMN07730213 + GSM2801757 + + + + + + + SRR6124471 + GSM2801757_r1 + + + + + + SRS2560850 + SAMN07730213 + GSM2801757 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237123 + + GSM2801756: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560849 + GSM2801756 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801756 + + + + + + + GEO Accession + GSM2801756 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560849 + SAMN07729847 + GSM2801756 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560849 + SAMN07729847 + GSM2801756 + + + + + + + SRR6124470 + GSM2801756_r1 + + + + + + SRS2560849 + SAMN07729847 + GSM2801756 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237122 + + GSM2801755: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560848 + GSM2801755 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801755 + + + + + + + GEO Accession + GSM2801755 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560848 + SAMN07729848 + GSM2801755 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560848 + SAMN07729848 + GSM2801755 + + + + + + + SRR6124469 + GSM2801755_r1 + + + + + + SRS2560848 + SAMN07729848 + GSM2801755 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237121 + + GSM2801754: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560847 + GSM2801754 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801754 + + + + + + + GEO Accession + GSM2801754 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560847 + SAMN07729849 + GSM2801754 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560847 + SAMN07729849 + GSM2801754 + + + + + + + SRR6124468 + GSM2801754_r1 + + + + + + SRS2560847 + SAMN07729849 + GSM2801754 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237120 + + GSM2801753: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560846 + GSM2801753 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801753 + + + + + + + GEO Accession + GSM2801753 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560846 + SAMN07729850 + GSM2801753 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560846 + SAMN07729850 + GSM2801753 + + + + + + + SRR6124467 + GSM2801753_r1 + + + + + + SRS2560846 + SAMN07729850 + GSM2801753 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237119 + + GSM2801752: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560845 + GSM2801752 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801752 + + + + + + + GEO Accession + GSM2801752 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560845 + SAMN07729851 + GSM2801752 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1h1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560845 + SAMN07729851 + GSM2801752 + + + + + + + SRR6124466 + GSM2801752_r1 + + + + + + SRS2560845 + SAMN07729851 + GSM2801752 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237118 + + GSM2801751: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560843 + GSM2801751 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801751 + + + + + + + GEO Accession + GSM2801751 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560843 + SAMN07729852 + GSM2801751 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560843 + SAMN07729852 + GSM2801751 + + + + + + + SRR6124465 + GSM2801751_r1 + + + + + + SRS2560843 + SAMN07729852 + GSM2801751 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237117 + + GSM2801750: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560842 + GSM2801750 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801750 + + + + + + + GEO Accession + GSM2801750 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560842 + SAMN07729853 + GSM2801750 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560842 + SAMN07729853 + GSM2801750 + + + + + + + SRR6124464 + GSM2801750_r1 + + + + + + SRS2560842 + SAMN07729853 + GSM2801750 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237116 + + GSM2801749: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560841 + GSM2801749 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801749 + + + + + + + GEO Accession + GSM2801749 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560841 + SAMN07729854 + GSM2801749 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560841 + SAMN07729854 + GSM2801749 + + + + + + + SRR6124463 + GSM2801749_r1 + + + + + + SRS2560841 + SAMN07729854 + GSM2801749 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237115 + + GSM2801748: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560840 + GSM2801748 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801748 + + + + + + + GEO Accession + GSM2801748 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560840 + SAMN07729855 + GSM2801748 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560840 + SAMN07729855 + GSM2801748 + + + + + + + SRR6124462 + GSM2801748_r1 + + + + + + SRS2560840 + SAMN07729855 + GSM2801748 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237114 + + GSM2801747: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560839 + GSM2801747 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801747 + + + + + + + GEO Accession + GSM2801747 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560839 + SAMN07729856 + GSM2801747 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560839 + SAMN07729856 + GSM2801747 + + + + + + + SRR6124461 + GSM2801747_r1 + + + + + + SRS2560839 + SAMN07729856 + GSM2801747 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237113 + + GSM2801746: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560844 + GSM2801746 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801746 + + + + + + + GEO Accession + GSM2801746 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560844 + SAMN07729857 + GSM2801746 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560844 + SAMN07729857 + GSM2801746 + + + + + + + SRR6124460 + GSM2801746_r1 + + + + + + SRS2560844 + SAMN07729857 + GSM2801746 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237112 + + GSM2801745: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560837 + GSM2801745 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801745 + + + + + + + GEO Accession + GSM2801745 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560837 + SAMN07729858 + GSM2801745 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560837 + SAMN07729858 + GSM2801745 + + + + + + + SRR6124459 + GSM2801745_r1 + + + + + + SRS2560837 + SAMN07729858 + GSM2801745 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237111 + + GSM2801744: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560835 + GSM2801744 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801744 + + + + + + + GEO Accession + GSM2801744 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560835 + SAMN07729859 + GSM2801744 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560835 + SAMN07729859 + GSM2801744 + + + + + + + SRR6124458 + GSM2801744_r1 + + + + + + SRS2560835 + SAMN07729859 + GSM2801744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237110 + + GSM2801743: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560834 + GSM2801743 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801743 + + + + + + + GEO Accession + GSM2801743 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560834 + SAMN07729860 + GSM2801743 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560834 + SAMN07729860 + GSM2801743 + + + + + + + SRR6124457 + GSM2801743_r1 + + + + + + SRS2560834 + SAMN07729860 + GSM2801743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237109 + + GSM2801742: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560833 + GSM2801742 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801742 + + + + + + + GEO Accession + GSM2801742 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560833 + SAMN07729861 + GSM2801742 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560833 + SAMN07729861 + GSM2801742 + + + + + + + SRR6124456 + GSM2801742_r1 + + + + + + SRS2560833 + SAMN07729861 + GSM2801742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237108 + + GSM2801741: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560852 + GSM2801741 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801741 + + + + + + + GEO Accession + GSM2801741 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560852 + SAMN07729862 + GSM2801741 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560852 + SAMN07729862 + GSM2801741 + + + + + + + SRR6124455 + GSM2801741_r1 + + + + + + SRS2560852 + SAMN07729862 + GSM2801741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237107 + + GSM2801740: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560831 + GSM2801740 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801740 + + + + + + + GEO Accession + GSM2801740 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560831 + SAMN07729863 + GSM2801740 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1g1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560831 + SAMN07729863 + GSM2801740 + + + + + + + SRR6124454 + GSM2801740_r1 + + + + + + SRS2560831 + SAMN07729863 + GSM2801740 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237106 + + GSM2801739: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560830 + GSM2801739 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801739 + + + + + + + GEO Accession + GSM2801739 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560830 + SAMN07729864 + GSM2801739 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560830 + SAMN07729864 + GSM2801739 + + + + + + + SRR6124453 + GSM2801739_r1 + + + + + + SRS2560830 + SAMN07729864 + GSM2801739 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237105 + + GSM2801738: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560829 + GSM2801738 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801738 + + + + + + + GEO Accession + GSM2801738 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560829 + SAMN07729865 + GSM2801738 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560829 + SAMN07729865 + GSM2801738 + + + + + + + SRR6124452 + GSM2801738_r1 + + + + + + SRS2560829 + SAMN07729865 + GSM2801738 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237104 + + GSM2801737: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560838 + GSM2801737 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801737 + + + + + + + GEO Accession + GSM2801737 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560838 + SAMN07729866 + GSM2801737 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560838 + SAMN07729866 + GSM2801737 + + + + + + + SRR6124451 + GSM2801737_r1 + + + + + + SRS2560838 + SAMN07729866 + GSM2801737 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237103 + + GSM2801736: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560828 + GSM2801736 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801736 + + + + + + + GEO Accession + GSM2801736 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560828 + SAMN07729867 + GSM2801736 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560828 + SAMN07729867 + GSM2801736 + + + + + + + SRR6124450 + GSM2801736_r1 + + + + + + SRS2560828 + SAMN07729867 + GSM2801736 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237102 + + GSM2801735: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560836 + GSM2801735 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801735 + + + + + + + GEO Accession + GSM2801735 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560836 + SAMN07729868 + GSM2801735 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560836 + SAMN07729868 + GSM2801735 + + + + + + + SRR6124449 + GSM2801735_r1 + + + + + + SRS2560836 + SAMN07729868 + GSM2801735 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237101 + + GSM2801734: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560827 + GSM2801734 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801734 + + + + + + + GEO Accession + GSM2801734 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560827 + SAMN07729871 + GSM2801734 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560827 + SAMN07729871 + GSM2801734 + + + + + + + SRR6124448 + GSM2801734_r1 + + + + + + SRS2560827 + SAMN07729871 + GSM2801734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237100 + + GSM2801733: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560826 + GSM2801733 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801733 + + + + + + + GEO Accession + GSM2801733 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560826 + SAMN07729872 + GSM2801733 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560826 + SAMN07729872 + GSM2801733 + + + + + + + SRR6124447 + GSM2801733_r1 + + + + + + SRS2560826 + SAMN07729872 + GSM2801733 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237099 + + GSM2801732: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560825 + GSM2801732 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801732 + + + + + + + GEO Accession + GSM2801732 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560825 + SAMN07729873 + GSM2801732 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560825 + SAMN07729873 + GSM2801732 + + + + + + + SRR6124446 + GSM2801732_r1 + + + + + + SRS2560825 + SAMN07729873 + GSM2801732 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237098 + + GSM2801731: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560824 + GSM2801731 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801731 + + + + + + + GEO Accession + GSM2801731 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560824 + SAMN07729870 + GSM2801731 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560824 + SAMN07729870 + GSM2801731 + + + + + + + SRR6124445 + GSM2801731_r1 + + + + + + SRS2560824 + SAMN07729870 + GSM2801731 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237097 + + GSM2801730: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560823 + GSM2801730 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801730 + + + + + + + GEO Accession + GSM2801730 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560823 + SAMN07729869 + GSM2801730 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560823 + SAMN07729869 + GSM2801730 + + + + + + + SRR6124444 + GSM2801730_r1 + + + + + + SRS2560823 + SAMN07729869 + GSM2801730 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237096 + + GSM2801729: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560822 + GSM2801729 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801729 + + + + + + + GEO Accession + GSM2801729 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560822 + SAMN07730153 + GSM2801729 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560822 + SAMN07730153 + GSM2801729 + + + + + + + SRR6124443 + GSM2801729_r1 + + + + + + SRS2560822 + SAMN07730153 + GSM2801729 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237095 + + GSM2801728: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560821 + GSM2801728 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801728 + + + + + + + GEO Accession + GSM2801728 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560821 + SAMN07730155 + GSM2801728 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1f1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560821 + SAMN07730155 + GSM2801728 + + + + + + + SRR6124442 + GSM2801728_r1 + + + + + + SRS2560821 + SAMN07730155 + GSM2801728 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237094 + + GSM2801727: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560820 + GSM2801727 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801727 + + + + + + + GEO Accession + GSM2801727 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560820 + SAMN07730148 + GSM2801727 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560820 + SAMN07730148 + GSM2801727 + + + + + + + SRR6124441 + GSM2801727_r1 + + + + + + SRS2560820 + SAMN07730148 + GSM2801727 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237093 + + GSM2801726: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560832 + GSM2801726 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801726 + + + + + + + GEO Accession + GSM2801726 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560832 + SAMN07730147 + GSM2801726 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560832 + SAMN07730147 + GSM2801726 + + + + + + + SRR6124440 + GSM2801726_r1 + + + + + + SRS2560832 + SAMN07730147 + GSM2801726 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237092 + + GSM2801725: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560819 + GSM2801725 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801725 + + + + + + + GEO Accession + GSM2801725 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560819 + SAMN07730149 + GSM2801725 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560819 + SAMN07730149 + GSM2801725 + + + + + + + SRR6124439 + GSM2801725_r1 + + + + + + SRS2560819 + SAMN07730149 + GSM2801725 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237091 + + GSM2801724: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560818 + GSM2801724 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801724 + + + + + + + GEO Accession + GSM2801724 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560818 + SAMN07729874 + GSM2801724 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560818 + SAMN07729874 + GSM2801724 + + + + + + + SRR6124438 + GSM2801724_r1 + + + + + + SRS2560818 + SAMN07729874 + GSM2801724 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237090 + + GSM2801723: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560817 + GSM2801723 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801723 + + + + + + + GEO Accession + GSM2801723 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560817 + SAMN07730152 + GSM2801723 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560817 + SAMN07730152 + GSM2801723 + + + + + + + SRR6124437 + GSM2801723_r1 + + + + + + SRS2560817 + SAMN07730152 + GSM2801723 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237089 + + GSM2801722: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560815 + GSM2801722 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801722 + + + + + + + GEO Accession + GSM2801722 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560815 + SAMN07730157 + GSM2801722 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560815 + SAMN07730157 + GSM2801722 + + + + + + + SRR6124436 + GSM2801722_r1 + + + + + + SRS2560815 + SAMN07730157 + GSM2801722 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237088 + + GSM2801721: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560816 + GSM2801721 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801721 + + + + + + + GEO Accession + GSM2801721 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560816 + SAMN07730154 + GSM2801721 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560816 + SAMN07730154 + GSM2801721 + + + + + + + SRR6124435 + GSM2801721_r1 + + + + + + SRS2560816 + SAMN07730154 + GSM2801721 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237087 + + GSM2801720: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560814 + GSM2801720 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801720 + + + + + + + GEO Accession + GSM2801720 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560814 + SAMN07730158 + GSM2801720 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560814 + SAMN07730158 + GSM2801720 + + + + + + + SRR6124434 + GSM2801720_r1 + + + + + + SRS2560814 + SAMN07730158 + GSM2801720 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237086 + + GSM2801719: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560813 + GSM2801719 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801719 + + + + + + + GEO Accession + GSM2801719 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560813 + SAMN07730159 + GSM2801719 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560813 + SAMN07730159 + GSM2801719 + + + + + + + SRR6124433 + GSM2801719_r1 + + + + + + SRS2560813 + SAMN07730159 + GSM2801719 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237085 + + GSM2801718: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560812 + GSM2801718 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801718 + + + + + + + GEO Accession + GSM2801718 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560812 + SAMN07730160 + GSM2801718 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560812 + SAMN07730160 + GSM2801718 + + + + + + + SRR6124432 + GSM2801718_r1 + + + + + + SRS2560812 + SAMN07730160 + GSM2801718 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237084 + + GSM2801717: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560811 + GSM2801717 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801717 + + + + + + + GEO Accession + GSM2801717 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560811 + SAMN07730151 + GSM2801717 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560811 + SAMN07730151 + GSM2801717 + + + + + + + SRR6124431 + GSM2801717_r1 + + + + + + SRS2560811 + SAMN07730151 + GSM2801717 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237083 + + GSM2801716: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560810 + GSM2801716 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801716 + + + + + + + GEO Accession + GSM2801716 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560810 + SAMN07730150 + GSM2801716 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1e1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560810 + SAMN07730150 + GSM2801716 + + + + + + + SRR6124430 + GSM2801716_r1 + + + + + + SRS2560810 + SAMN07730150 + GSM2801716 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237082 + + GSM2801715: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560809 + GSM2801715 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801715 + + + + + + + GEO Accession + GSM2801715 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560809 + SAMN07730162 + GSM2801715 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560809 + SAMN07730162 + GSM2801715 + + + + + + + SRR6124429 + GSM2801715_r1 + + + + + + SRS2560809 + SAMN07730162 + GSM2801715 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237081 + + GSM2801714: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560808 + GSM2801714 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801714 + + + + + + + GEO Accession + GSM2801714 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560808 + SAMN07730163 + GSM2801714 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560808 + SAMN07730163 + GSM2801714 + + + + + + + SRR6124428 + GSM2801714_r1 + + + + + + SRS2560808 + SAMN07730163 + GSM2801714 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237080 + + GSM2801713: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560806 + GSM2801713 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801713 + + + + + + + GEO Accession + GSM2801713 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560806 + SAMN07730164 + GSM2801713 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560806 + SAMN07730164 + GSM2801713 + + + + + + + SRR6124427 + GSM2801713_r1 + + + + + + SRS2560806 + SAMN07730164 + GSM2801713 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237079 + + GSM2801712: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560807 + GSM2801712 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801712 + + + + + + + GEO Accession + GSM2801712 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560807 + SAMN07730165 + GSM2801712 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560807 + SAMN07730165 + GSM2801712 + + + + + + + SRR6124426 + GSM2801712_r1 + + + + + + SRS2560807 + SAMN07730165 + GSM2801712 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237078 + + GSM2801711: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560805 + GSM2801711 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801711 + + + + + + + GEO Accession + GSM2801711 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560805 + SAMN07730167 + GSM2801711 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560805 + SAMN07730167 + GSM2801711 + + + + + + + SRR6124425 + GSM2801711_r1 + + + + + + SRS2560805 + SAMN07730167 + GSM2801711 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237077 + + GSM2801710: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560804 + GSM2801710 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801710 + + + + + + + GEO Accession + GSM2801710 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560804 + SAMN07730156 + GSM2801710 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560804 + SAMN07730156 + GSM2801710 + + + + + + + SRR6124424 + GSM2801710_r1 + + + + + + SRS2560804 + SAMN07730156 + GSM2801710 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237076 + + GSM2801709: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560803 + GSM2801709 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801709 + + + + + + + GEO Accession + GSM2801709 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560803 + SAMN07730166 + GSM2801709 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560803 + SAMN07730166 + GSM2801709 + + + + + + + SRR6124423 + GSM2801709_r1 + + + + + + SRS2560803 + SAMN07730166 + GSM2801709 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237075 + + GSM2801708: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560802 + GSM2801708 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801708 + + + + + + + GEO Accession + GSM2801708 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560802 + SAMN07730171 + GSM2801708 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560802 + SAMN07730171 + GSM2801708 + + + + + + + SRR6124422 + GSM2801708_r1 + + + + + + SRS2560802 + SAMN07730171 + GSM2801708 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237074 + + GSM2801707: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560801 + GSM2801707 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801707 + + + + + + + GEO Accession + GSM2801707 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560801 + SAMN07730161 + GSM2801707 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560801 + SAMN07730161 + GSM2801707 + + + + + + + SRR6124421 + GSM2801707_r1 + + + + + + SRS2560801 + SAMN07730161 + GSM2801707 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237073 + + GSM2801706: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560800 + GSM2801706 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801706 + + + + + + + GEO Accession + GSM2801706 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560800 + SAMN07730182 + GSM2801706 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560800 + SAMN07730182 + GSM2801706 + + + + + + + SRR6124420 + GSM2801706_r1 + + + + + + SRS2560800 + SAMN07730182 + GSM2801706 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237072 + + GSM2801705: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560799 + GSM2801705 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801705 + + + + + + + GEO Accession + GSM2801705 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560799 + SAMN07730183 + GSM2801705 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560799 + SAMN07730183 + GSM2801705 + + + + + + + SRR6124419 + GSM2801705_r1 + + + + + + SRS2560799 + SAMN07730183 + GSM2801705 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237071 + + GSM2801704: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560798 + GSM2801704 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801704 + + + + + + + GEO Accession + GSM2801704 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560798 + SAMN07730181 + GSM2801704 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1d1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560798 + SAMN07730181 + GSM2801704 + + + + + + + SRR6124418 + GSM2801704_r1 + + + + + + SRS2560798 + SAMN07730181 + GSM2801704 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237070 + + GSM2801703: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560796 + GSM2801703 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801703 + + + + + + + GEO Accession + GSM2801703 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560796 + SAMN07730170 + GSM2801703 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560796 + SAMN07730170 + GSM2801703 + + + + + + + SRR6124417 + GSM2801703_r1 + + + + + + SRS2560796 + SAMN07730170 + GSM2801703 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237069 + + GSM2801702: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560795 + GSM2801702 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801702 + + + + + + + GEO Accession + GSM2801702 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560795 + SAMN07730172 + GSM2801702 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560795 + SAMN07730172 + GSM2801702 + + + + + + + SRR6124416 + GSM2801702_r1 + + + + + + SRS2560795 + SAMN07730172 + GSM2801702 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237068 + + GSM2801701: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560794 + GSM2801701 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801701 + + + + + + + GEO Accession + GSM2801701 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560794 + SAMN07730173 + GSM2801701 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560794 + SAMN07730173 + GSM2801701 + + + + + + + SRR6124415 + GSM2801701_r1 + + + + + + SRS2560794 + SAMN07730173 + GSM2801701 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237067 + + GSM2801700: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560793 + GSM2801700 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801700 + + + + + + + GEO Accession + GSM2801700 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560793 + SAMN07730174 + GSM2801700 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560793 + SAMN07730174 + GSM2801700 + + + + + + + SRR6124414 + GSM2801700_r1 + + + + + + SRS2560793 + SAMN07730174 + GSM2801700 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237066 + + GSM2801699: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560791 + GSM2801699 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801699 + + + + + + + GEO Accession + GSM2801699 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560791 + SAMN07730175 + GSM2801699 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560791 + SAMN07730175 + GSM2801699 + + + + + + + SRR6124413 + GSM2801699_r1 + + + + + + SRS2560791 + SAMN07730175 + GSM2801699 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237065 + + GSM2801698: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560792 + GSM2801698 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801698 + + + + + + + GEO Accession + GSM2801698 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560792 + SAMN07730176 + GSM2801698 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560792 + SAMN07730176 + GSM2801698 + + + + + + + SRR6124412 + GSM2801698_r1 + + + + + + SRS2560792 + SAMN07730176 + GSM2801698 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237064 + + GSM2801697: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560790 + GSM2801697 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801697 + + + + + + + GEO Accession + GSM2801697 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560790 + SAMN07730177 + GSM2801697 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560790 + SAMN07730177 + GSM2801697 + + + + + + + SRR6124411 + GSM2801697_r1 + + + + + + SRS2560790 + SAMN07730177 + GSM2801697 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237063 + + GSM2801696: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560789 + GSM2801696 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801696 + + + + + + + GEO Accession + GSM2801696 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560789 + SAMN07730169 + GSM2801696 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560789 + SAMN07730169 + GSM2801696 + + + + + + + SRR6124410 + GSM2801696_r1 + + + + + + SRS2560789 + SAMN07730169 + GSM2801696 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237062 + + GSM2801695: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560788 + GSM2801695 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801695 + + + + + + + GEO Accession + GSM2801695 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560788 + SAMN07729917 + GSM2801695 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560788 + SAMN07729917 + GSM2801695 + + + + + + + SRR6124409 + GSM2801695_r1 + + + + + + SRS2560788 + SAMN07729917 + GSM2801695 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237061 + + GSM2801694: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560787 + GSM2801694 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801694 + + + + + + + GEO Accession + GSM2801694 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560787 + SAMN07730180 + GSM2801694 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560787 + SAMN07730180 + GSM2801694 + + + + + + + SRR6124408 + GSM2801694_r1 + + + + + + SRS2560787 + SAMN07730180 + GSM2801694 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237060 + + GSM2801693: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560786 + GSM2801693 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801693 + + + + + + + GEO Accession + GSM2801693 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560786 + SAMN07730168 + GSM2801693 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560786 + SAMN07730168 + GSM2801693 + + + + + + + SRR6124407 + GSM2801693_r1 + + + + + + SRS2560786 + SAMN07730168 + GSM2801693 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237059 + + GSM2801692: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560785 + GSM2801692 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801692 + + + + + + + GEO Accession + GSM2801692 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560785 + SAMN07730179 + GSM2801692 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1c1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560785 + SAMN07730179 + GSM2801692 + + + + + + + SRR6124406 + GSM2801692_r1 + + + + + + SRS2560785 + SAMN07730179 + GSM2801692 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237058 + + GSM2801691: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560784 + GSM2801691 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801691 + + + + + + + GEO Accession + GSM2801691 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560784 + SAMN07730178 + GSM2801691 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560784 + SAMN07730178 + GSM2801691 + + + + + + + SRR6124405 + GSM2801691_r1 + + + + + + SRS2560784 + SAMN07730178 + GSM2801691 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237057 + + GSM2801690: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560783 + GSM2801690 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801690 + + + + + + + GEO Accession + GSM2801690 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560783 + SAMN07729912 + GSM2801690 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560783 + SAMN07729912 + GSM2801690 + + + + + + + SRR6124404 + GSM2801690_r1 + + + + + + SRS2560783 + SAMN07729912 + GSM2801690 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237056 + + GSM2801689: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560782 + GSM2801689 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801689 + + + + + + + GEO Accession + GSM2801689 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560782 + SAMN07729913 + GSM2801689 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560782 + SAMN07729913 + GSM2801689 + + + + + + + SRR6124403 + GSM2801689_r1 + + + + + + SRS2560782 + SAMN07729913 + GSM2801689 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237055 + + GSM2801688: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560781 + GSM2801688 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801688 + + + + + + + GEO Accession + GSM2801688 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560781 + SAMN07729914 + GSM2801688 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560781 + SAMN07729914 + GSM2801688 + + + + + + + SRR6124402 + GSM2801688_r1 + + + + + + SRS2560781 + SAMN07729914 + GSM2801688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237054 + + GSM2801687: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560780 + GSM2801687 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801687 + + + + + + + GEO Accession + GSM2801687 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560780 + SAMN07729915 + GSM2801687 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560780 + SAMN07729915 + GSM2801687 + + + + + + + SRR6124401 + GSM2801687_r1 + + + + + + SRS2560780 + SAMN07729915 + GSM2801687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237053 + + GSM2801686: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560779 + GSM2801686 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801686 + + + + + + + GEO Accession + GSM2801686 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560779 + SAMN07729916 + GSM2801686 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560779 + SAMN07729916 + GSM2801686 + + + + + + + SRR6124400 + GSM2801686_r1 + + + + + + SRS2560779 + SAMN07729916 + GSM2801686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237052 + + GSM2801685: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560778 + GSM2801685 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801685 + + + + + + + GEO Accession + GSM2801685 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560778 + SAMN07729918 + GSM2801685 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560778 + SAMN07729918 + GSM2801685 + + + + + + + SRR6124399 + GSM2801685_r1 + + + + + + SRS2560778 + SAMN07729918 + GSM2801685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237051 + + GSM2801684: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560777 + GSM2801684 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801684 + + + + + + + GEO Accession + GSM2801684 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560777 + SAMN07729907 + GSM2801684 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560777 + SAMN07729907 + GSM2801684 + + + + + + + SRR6124398 + GSM2801684_r1 + + + + + + SRS2560777 + SAMN07729907 + GSM2801684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237050 + + GSM2801683: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560776 + GSM2801683 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801683 + + + + + + + GEO Accession + GSM2801683 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560776 + SAMN07729908 + GSM2801683 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560776 + SAMN07729908 + GSM2801683 + + + + + + + SRR6124397 + GSM2801683_r1 + + + + + + SRS2560776 + SAMN07729908 + GSM2801683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237049 + + GSM2801682: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560775 + GSM2801682 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801682 + + + + + + + GEO Accession + GSM2801682 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560775 + SAMN07729906 + GSM2801682 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560775 + SAMN07729906 + GSM2801682 + + + + + + + SRR6124396 + GSM2801682_r1 + + + + + + SRS2560775 + SAMN07729906 + GSM2801682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237048 + + GSM2801681: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560774 + GSM2801681 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801681 + + + + + + + GEO Accession + GSM2801681 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560774 + SAMN07729910 + GSM2801681 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560774 + SAMN07729910 + GSM2801681 + + + + + + + SRR6124395 + GSM2801681_r1 + + + + + + SRS2560774 + SAMN07729910 + GSM2801681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237047 + + GSM2801680: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560773 + GSM2801680 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801680 + + + + + + + GEO Accession + GSM2801680 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560773 + SAMN07729909 + GSM2801680 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1b1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560773 + SAMN07729909 + GSM2801680 + + + + + + + SRR6124394 + GSM2801680_r1 + + + + + + SRS2560773 + SAMN07729909 + GSM2801680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237046 + + GSM2801679: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a9; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560772 + GSM2801679 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801679 + + + + + + + GEO Accession + GSM2801679 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560772 + SAMN07729911 + GSM2801679 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a9 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560772 + SAMN07729911 + GSM2801679 + + + + + + + SRR6124393 + GSM2801679_r1 + + + + + + SRS2560772 + SAMN07729911 + GSM2801679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237045 + + GSM2801678: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a8; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560771 + GSM2801678 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801678 + + + + + + + GEO Accession + GSM2801678 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560771 + SAMN07729839 + GSM2801678 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a8 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560771 + SAMN07729839 + GSM2801678 + + + + + + + SRR6124392 + GSM2801678_r1 + + + + + + SRS2560771 + SAMN07729839 + GSM2801678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237044 + + GSM2801677: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a7; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560770 + GSM2801677 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801677 + + + + + + + GEO Accession + GSM2801677 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560770 + SAMN07729841 + GSM2801677 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a7 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560770 + SAMN07729841 + GSM2801677 + + + + + + + SRR6124391 + GSM2801677_r1 + + + + + + SRS2560770 + SAMN07729841 + GSM2801677 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237043 + + GSM2801676: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a6; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560769 + GSM2801676 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801676 + + + + + + + GEO Accession + GSM2801676 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560769 + SAMN07729842 + GSM2801676 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a6 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560769 + SAMN07729842 + GSM2801676 + + + + + + + SRR6124390 + GSM2801676_r1 + + + + + + SRS2560769 + SAMN07729842 + GSM2801676 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237042 + + GSM2801675: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a5; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560768 + GSM2801675 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801675 + + + + + + + GEO Accession + GSM2801675 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560768 + SAMN07729843 + GSM2801675 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a5 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560768 + SAMN07729843 + GSM2801675 + + + + + + + SRR6124389 + GSM2801675_r1 + + + + + + SRS2560768 + SAMN07729843 + GSM2801675 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237041 + + GSM2801674: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a4; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560767 + GSM2801674 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801674 + + + + + + + GEO Accession + GSM2801674 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560767 + SAMN07729844 + GSM2801674 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a4 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560767 + SAMN07729844 + GSM2801674 + + + + + + + SRR6124388 + GSM2801674_r1 + + + + + + SRS2560767 + SAMN07729844 + GSM2801674 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237040 + + GSM2801673: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a3; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560766 + GSM2801673 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801673 + + + + + + + GEO Accession + GSM2801673 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560766 + SAMN07729840 + GSM2801673 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a3 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560766 + SAMN07729840 + GSM2801673 + + + + + + + SRR6124387 + GSM2801673_r1 + + + + + + SRS2560766 + SAMN07729840 + GSM2801673 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237039 + + GSM2801672: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a2; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560765 + GSM2801672 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801672 + + + + + + + GEO Accession + GSM2801672 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560765 + SAMN07730214 + GSM2801672 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a2 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560765 + SAMN07730214 + GSM2801672 + + + + + + + SRR6124386 + GSM2801672_r1 + + + + + + SRS2560765 + SAMN07730214 + GSM2801672 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237038 + + GSM2801671: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a12; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560764 + GSM2801671 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801671 + + + + + + + GEO Accession + GSM2801671 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560764 + SAMN07730215 + GSM2801671 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a12 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560764 + SAMN07730215 + GSM2801671 + + + + + + + SRR6124385 + GSM2801671_r1 + + + + + + SRS2560764 + SAMN07730215 + GSM2801671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237037 + + GSM2801670: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a11; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560763 + GSM2801670 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801670 + + + + + + + GEO Accession + GSM2801670 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560763 + SAMN07729835 + GSM2801670 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a11 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560763 + SAMN07729835 + GSM2801670 + + + + + + + SRR6124384 + GSM2801670_r1 + + + + + + SRS2560763 + SAMN07729835 + GSM2801670 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237036 + + GSM2801669: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a10; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560762 + GSM2801669 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801669 + + + + + + + GEO Accession + GSM2801669 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560762 + SAMN07729836 + GSM2801669 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a10 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560762 + SAMN07729836 + GSM2801669 + + + + + + + SRR6124383 + GSM2801669_r1 + + + + + + SRS2560762 + SAMN07729836 + GSM2801669 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237035 + + GSM2801668: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a1; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560761 + GSM2801668 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801668 + + + + + + + GEO Accession + GSM2801668 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560761 + SAMN07729837 + GSM2801668 + + HEK293 scRNA-Seq Plate1 HEK293_SC_P1a1 + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Single cell from cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560761 + SAMN07729837 + GSM2801668 + + + + + + + SRR6124382 + GSM2801668_r1 + + + + + + SRS2560761 + SAMN07729837 + GSM2801668 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX3237034 + + GSM2801667: HEK293 RNA-Seq HEK293_BK; Homo sapiens; RNA-Seq + + + SRP119249 + + + + + + + SRS2560760 + GSM2801667 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + published scPLATE-Seq protocol published scPLATE-Seq protocol + + + + + NextSeq 500 + + + + + + gds + 302801667 + + + + + + + GEO Accession + GSM2801667 + + + + + + SRA616325 + GEO: GSE104493 + + + + NCBI + + + Geo + Curators + + + + + + SRP119249 + PRJNA412850 + GSE104493 + + + Benchmark Data for scPLATE-Seq + + Generate benchmark data for scPLATE-Seq Overall design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture. + GSE104493 + + + + + SRS2560760 + SAMN07729838 + GSM2801667 + + HEK293 RNA-Seq HEK293_BK + + 9606 + Homo sapiens + + + + + bioproject + 412850 + + + + + + + source_name + Cultured HEK293 cells + + + cell line + HEK293 + + + + + + + SRS2560760 + SAMN07729838 + GSM2801667 + + + + + + + SRR6124381 + GSM2801667_r1 + + + + + + SRS2560760 + SAMN07729838 + GSM2801667 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE125536.xml b/tests/data/GSE125536.xml new file mode 100644 index 0000000..ea8dd71 --- /dev/null +++ b/tests/data/GSE125536.xml @@ -0,0 +1,390 @@ + + + + + + + SRX5284012 + + GSM3576734: ESC timecourse_0-72hours; Mus musculus; RNA-Seq + + + SRP181689 + PRJNA516696 + + + + + + + SRS4283730 + SAMN10794338 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044) RNA libraries were prepared for sequencing by the indrop core facility at Harvard Medical School. We used library version v3 where R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail. Library index for LIB1 (ESC 0hr) is:ATAGAGAG , LIB2 (ESC 24hr) is: AGAGGATA, LIB3 (ESC 48hr) is:CTCCTTAC and LIB4 (ESC 72hr) is TATGCAGT. + + + + + NextSeq 500 + + + + + + gds + 303576734 + + + + + + + GEO Accession + GSM3576734 + + + + + + SRA838328 + GEO: GSE125536 + + + + NCBI + + + Geo + Curators + + + + + + SRP181689 + PRJNA516696 + GSE125536 + + + Generation of chemically induced totipotent cells through multi-parametric analysis of single-cells + + Pluripotent stem cells fluctuate among distinct functional cell states. Such heterogeneity undermines the potential applications of stem cells in regenerative medicine. The heterogeneity of pluripotent cell states and their molecular nature remain less understood. Here, we utilized mass cytometry to dissect pluripotent cell states by simultaneously profiling multiple proteins and their modifications in single cells. Results indicated the role of extensive signaling cross-talk among multiple pathways in regulating cell state heterogeneity. By systematically dissecting the signals and their combinations, we identify conditions through which large portions of pluripotent cells can be chemically reprogrammed into totipotent cells which can be cultured. Unlike pluripotent cells, these chemically induced totipotent cells (CiTC) give rise to both embryonic and extra-embryonic cell types. In addition, CiTCs are molecularly distinct from pluripotent cells. CiTCs provide an in-vitro model to understand the nature of totipotent cells and the plasticity of pluripotent cells. Our quantitative and integrative approach provides general method to understand similar heterogenous cell systems such as cancer. Overall design: Single-cell RNA-sequencing of a time-course of embryonic stem cells (ESC) under cell culture conditions to induce the totipotent-like cells + GSE125536 + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + ESC timecourse_0-72hours + + 10090 + Mus musculus + + + + + bioproject + 516696 + + + + + + + source_name + Embryonic Stem Cells + + + cell type + ESC + + + treatment + totipotent culture conditions + + + time + mixed sample (non-demultiplexed) representing timepoints 0h, 24h, 48h, 72h + + + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + + + + + + SRR8479162 + GSM3576734_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=BTTT --read1PairFiles=SUB05757_S1_L001_R1_001.fastq.gz --read2PairFiles=SUB05757_S1_L001_R2_001.fastq.gz --read3PairFiles=SUB05757_S1_L001_R3_001.fastq.gz --read4PairFiles=SUB05757_S1_L001_R4_001.fastq.gz + + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR8479163 + GSM3576734_r2 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=BTTT --read1PairFiles=SUB05757_S1_L002_R1_001.fastq.gz --read2PairFiles=SUB05757_S1_L002_R2_001.fastq.gz --read3PairFiles=SUB05757_S1_L002_R3_001.fastq.gz --read4PairFiles=SUB05757_S1_L002_R4_001.fastq.gz + + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR8479164 + GSM3576734_r3 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=BTTT --read1PairFiles=SUB05757_S1_L003_R1_001.fastq.gz --read2PairFiles=SUB05757_S1_L003_R2_001.fastq.gz --read3PairFiles=SUB05757_S1_L003_R3_001.fastq.gz --read4PairFiles=SUB05757_S1_L003_R4_001.fastq.gz + + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR8479165 + GSM3576734_r4 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=BTTT --read1PairFiles=SUB05757_S1_L004_R1_001.fastq.gz --read2PairFiles=SUB05757_S1_L004_R2_001.fastq.gz --read3PairFiles=SUB05757_S1_L004_R3_001.fastq.gz --read4PairFiles=SUB05757_S1_L004_R4_001.fastq.gz + + + + + + SRS4283730 + SAMN10794338 + GSM3576734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE128117.xml b/tests/data/GSE128117.xml new file mode 100644 index 0000000..e3cb4f0 --- /dev/null +++ b/tests/data/GSE128117.xml @@ -0,0 +1,4468 @@ + + + + + + + SRX5503391 + + GSM3665202: D712rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471946 + GSM3665202 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665202 + + + + + + + GEO Accession + GSM3665202 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471946 + SAMN11099526 + GSM3665202 + + D712rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP negative + + + + + + + SRS4471946 + SAMN11099526 + GSM3665202 + + + + + + + SRR8707971 + GSM3665202_r1 + + + + + + SRS4471946 + SAMN11099526 + GSM3665202 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503390 + + GSM3665201: D711rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471945 + GSM3665201 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665201 + + + + + + + GEO Accession + GSM3665201 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471945 + SAMN11099527 + GSM3665201 + + D711rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP positive + + + + + + + SRS4471945 + SAMN11099527 + GSM3665201 + + + + + + + SRR8707970 + GSM3665201_r1 + + + + + + SRS4471945 + SAMN11099527 + GSM3665201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503389 + + GSM3665200: D710rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471944 + GSM3665200 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665200 + + + + + + + GEO Accession + GSM3665200 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471944 + SAMN11099528 + GSM3665200 + + D710rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP negative + + + + + + + SRS4471944 + SAMN11099528 + GSM3665200 + + + + + + + SRR8707969 + GSM3665200_r1 + + + + + + SRS4471944 + SAMN11099528 + GSM3665200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503388 + + GSM3665199: D709rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471943 + GSM3665199 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665199 + + + + + + + GEO Accession + GSM3665199 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471943 + SAMN11099529 + GSM3665199 + + D709rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP positive + + + + + + + SRS4471943 + SAMN11099529 + GSM3665199 + + + + + + + SRR8707968 + GSM3665199_r1 + + + + + + SRS4471943 + SAMN11099529 + GSM3665199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503387 + + GSM3665198: D708rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471942 + GSM3665198 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665198 + + + + + + + GEO Accession + GSM3665198 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471942 + SAMN11099530 + GSM3665198 + + D708rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP negative + + + + + + + SRS4471942 + SAMN11099530 + GSM3665198 + + + + + + + SRR8707967 + GSM3665198_r1 + + + + + + SRS4471942 + SAMN11099530 + GSM3665198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503386 + + GSM3665197: D707rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471941 + GSM3665197 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665197 + + + + + + + GEO Accession + GSM3665197 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471941 + SAMN11099531 + GSM3665197 + + D707rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP positive + + + + + + + SRS4471941 + SAMN11099531 + GSM3665197 + + + + + + + SRR8707966 + GSM3665197_r1 + + + + + + SRS4471941 + SAMN11099531 + GSM3665197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503385 + + GSM3665196: D706rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471940 + GSM3665196 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665196 + + + + + + + GEO Accession + GSM3665196 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471940 + SAMN11099532 + GSM3665196 + + D706rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP negative + + + + + + + SRS4471940 + SAMN11099532 + GSM3665196 + + + + + + + SRR8707965 + GSM3665196_r1 + + + + + + SRS4471940 + SAMN11099532 + GSM3665196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503384 + + GSM3665195: D705rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471939 + GSM3665195 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665195 + + + + + + + GEO Accession + GSM3665195 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471939 + SAMN11099533 + GSM3665195 + + D705rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP positive + + + + + + + SRS4471939 + SAMN11099533 + GSM3665195 + + + + + + + SRR8707964 + GSM3665195_r1 + + + + + + SRS4471939 + SAMN11099533 + GSM3665195 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503383 + + GSM3665194: D704rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471938 + GSM3665194 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665194 + + + + + + + GEO Accession + GSM3665194 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471938 + SAMN11099534 + GSM3665194 + + D704rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP negative + + + + + + + SRS4471938 + SAMN11099534 + GSM3665194 + + + + + + + SRR8707963 + GSM3665194_r1 + + + + + + SRS4471938 + SAMN11099534 + GSM3665194 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503382 + + GSM3665193: D703rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471937 + GSM3665193 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665193 + + + + + + + GEO Accession + GSM3665193 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471937 + SAMN11099535 + GSM3665193 + + D703rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP positive + + + + + + + SRS4471937 + SAMN11099535 + GSM3665193 + + + + + + + SRR8707962 + GSM3665193_r1 + + + + + + SRS4471937 + SAMN11099535 + GSM3665193 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503381 + + GSM3665192: D702rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471936 + GSM3665192 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665192 + + + + + + + GEO Accession + GSM3665192 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471936 + SAMN11099536 + GSM3665192 + + D702rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP negative + + + + + + + SRS4471936 + SAMN11099536 + GSM3665192 + + + + + + + SRR8707961 + GSM3665192_r1 + + + + + + SRS4471936 + SAMN11099536 + GSM3665192 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503380 + + GSM3665191: D701rna_D502rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471935 + GSM3665191 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665191 + + + + + + + GEO Accession + GSM3665191 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471935 + SAMN11099537 + GSM3665191 + + D701rna_D502rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP positive + + + + + + + SRS4471935 + SAMN11099537 + GSM3665191 + + + + + + + SRR8707960 + GSM3665191_r1 + + + + + + SRS4471935 + SAMN11099537 + GSM3665191 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503379 + + GSM3665190: D712rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471934 + GSM3665190 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665190 + + + + + + + GEO Accession + GSM3665190 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471934 + SAMN11099538 + GSM3665190 + + D712rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP negative + + + + + + + SRS4471934 + SAMN11099538 + GSM3665190 + + + + + + + SRR8707959 + GSM3665190_r1 + + + + + + SRS4471934 + SAMN11099538 + GSM3665190 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503378 + + GSM3665189: D711rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471933 + GSM3665189 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665189 + + + + + + + GEO Accession + GSM3665189 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471933 + SAMN11099539 + GSM3665189 + + D711rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP positive + + + + + + + SRS4471933 + SAMN11099539 + GSM3665189 + + + + + + + SRR8707958 + GSM3665189_r1 + + + + + + SRS4471933 + SAMN11099539 + GSM3665189 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503377 + + GSM3665188: D710rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471932 + GSM3665188 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665188 + + + + + + + GEO Accession + GSM3665188 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471932 + SAMN11099540 + GSM3665188 + + D710rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP negative + + + + + + + SRS4471932 + SAMN11099540 + GSM3665188 + + + + + + + SRR8707957 + GSM3665188_r1 + + + + + + SRS4471932 + SAMN11099540 + GSM3665188 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503376 + + GSM3665187: D709rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471931 + GSM3665187 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665187 + + + + + + + GEO Accession + GSM3665187 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471931 + SAMN11099541 + GSM3665187 + + D709rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP positive + + + + + + + SRS4471931 + SAMN11099541 + GSM3665187 + + + + + + + SRR8707956 + GSM3665187_r1 + + + + + + SRS4471931 + SAMN11099541 + GSM3665187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503375 + + GSM3665186: D708rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471930 + GSM3665186 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665186 + + + + + + + GEO Accession + GSM3665186 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471930 + SAMN11099542 + GSM3665186 + + D708rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP negative + + + + + + + SRS4471930 + SAMN11099542 + GSM3665186 + + + + + + + SRR8707955 + GSM3665186_r1 + + + + + + SRS4471930 + SAMN11099542 + GSM3665186 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503374 + + GSM3665185: D707rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471929 + GSM3665185 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665185 + + + + + + + GEO Accession + GSM3665185 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471929 + SAMN11099543 + GSM3665185 + + D707rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Colon + + + strain + Guca2a-Venus + + + tissue + Colon + + + genotype/variation + GFP positive + + + + + + + SRS4471929 + SAMN11099543 + GSM3665185 + + + + + + + SRR8707954 + GSM3665185_r1 + + + + + + SRS4471929 + SAMN11099543 + GSM3665185 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503373 + + GSM3665184: D706rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471928 + GSM3665184 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665184 + + + + + + + GEO Accession + GSM3665184 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471928 + SAMN11099544 + GSM3665184 + + D706rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP negative + + + + + + + SRS4471928 + SAMN11099544 + GSM3665184 + + + + + + + SRR8707953 + GSM3665184_r1 + + + + + + SRS4471928 + SAMN11099544 + GSM3665184 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503372 + + GSM3665183: D705rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471927 + GSM3665183 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665183 + + + + + + + GEO Accession + GSM3665183 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471927 + SAMN11099545 + GSM3665183 + + D705rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Ileum + + + strain + Guca2a-Venus + + + tissue + Ileum + + + genotype/variation + GFP positive + + + + + + + SRS4471927 + SAMN11099545 + GSM3665183 + + + + + + + SRR8707952 + GSM3665183_r1 + + + + + + SRS4471927 + SAMN11099545 + GSM3665183 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503371 + + GSM3665182: D704rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471926 + GSM3665182 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665182 + + + + + + + GEO Accession + GSM3665182 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471926 + SAMN11099546 + GSM3665182 + + D704rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP negative + + + + + + + SRS4471926 + SAMN11099546 + GSM3665182 + + + + + + + SRR8707951 + GSM3665182_r1 + + + + + + SRS4471926 + SAMN11099546 + GSM3665182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503370 + + GSM3665181: D703rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471925 + GSM3665181 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665181 + + + + + + + GEO Accession + GSM3665181 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471925 + SAMN11099547 + GSM3665181 + + D703rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Jejunum + + + strain + Guca2a-Venus + + + tissue + Jejunum + + + genotype/variation + GFP positive + + + + + + + SRS4471925 + SAMN11099547 + GSM3665181 + + + + + + + SRR8707950 + GSM3665181_r1 + + + + + + SRS4471925 + SAMN11099547 + GSM3665181 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503369 + + GSM3665180: D702rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471924 + GSM3665180 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665180 + + + + + + + GEO Accession + GSM3665180 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471924 + SAMN11099548 + GSM3665180 + + D702rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP negative + + + + + + + SRS4471924 + SAMN11099548 + GSM3665180 + + + + + + + SRR8707949 + GSM3665180_r1 + + + + + + SRS4471924 + SAMN11099548 + GSM3665180 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX5503368 + + GSM3665179: D701rna_D501rna; Mus musculus; RNA-Seq + + + SRP188103 + + + + + + + SRS4471923 + GSM3665179 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer 10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara) RNAseq SE-50 on an Illumina HiSEQ 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 303665179 + + + + + + + GEO Accession + GSM3665179 + + + + + + SRA858508 + GEO: GSE128117 + + + + NCBI + + + Geo + Curators + + + + + + SRP188103 + PRJNA526492 + GSE128117 + + + Characterization of Guca2a expressing cells in the mouse intestine + + We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract. Overall design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice) + GSE128117 + + + + + SRS4471923 + SAMN11099525 + GSM3665179 + + D701rna_D501rna + + 10090 + Mus musculus + + + + + bioproject + 526492 + + + + + + + source_name + Duodenum + + + strain + Guca2a-Venus + + + tissue + Duodenum + + + genotype/variation + GFP positive + + + + + + + SRS4471923 + SAMN11099525 + GSM3665179 + + + + + + + SRR8707948 + GSM3665179_r1 + + + + + + SRS4471923 + SAMN11099525 + GSM3665179 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE141784.xml b/tests/data/GSE141784.xml new file mode 100644 index 0000000..984d069 --- /dev/null +++ b/tests/data/GSE141784.xml @@ -0,0 +1,1937 @@ + + + + + + + SRX7341052 + + GSM4213202: NOD.Rag; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801122 + GSM4213202 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213202 + + + + + + + GEO Accession + GSM4213202 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801122 + SAMN13527342 + GSM4213202 + + NOD.Rag + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD.129S7(B6)-Rag1tm1Mom/J (NOD.Rag1-/-) + + + age + 8-16 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801122 + SAMN13527342 + GSM4213202 + + + + + + + SRR10662111 + GSM4213202_r1 + + + + + + SRS5801122 + SAMN13527342 + GSM4213202 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341051 + + GSM4213201: NOD.Ifngr1; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801121 + GSM4213201 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213201 + + + + + + + GEO Accession + GSM4213201 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801121 + SAMN13527343 + GSM4213201 + + NOD.Ifngr1 + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD.Ifngr1-/- + + + age + 8 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801121 + SAMN13527343 + GSM4213201 + + + + + + + SRR10662109 + GSM4213201_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD.Ifngr1_8w_S1_L001_I1_001.fastq.gz --read2PairFiles=NOD.Ifngr1_8w_S1_L001_R1_001.fastq.gz --read3PairFiles=NOD.Ifngr1_8w_S1_L001_R2_001.fastq.gz + + + + + + SRS5801121 + SAMN13527343 + GSM4213201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662110 + GSM4213201_r2 + + + + + loader + fastq-load.py + + + options + --useAndDiscardNames --readTypes=TTB --read1PairFiles=NOD.Ifngr1_8w_S1_L002_I1_001.fastq.gz --read2PairFiles=NOD.Ifngr1_8w_S1_L002_R1_001.fastq.gz --read3PairFiles=NOD.Ifngr1_8w_S1_L002_R2_001.fastq.gz + + + + + + SRS5801121 + SAMN13527343 + GSM4213201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341050 + + GSM4213200: NOD_8_wks_2; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801120 + GSM4213200 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213200 + + + + + + + GEO Accession + GSM4213200 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801120 + SAMN13527344 + GSM4213200 + + NOD_8_wks_2 + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD/ShiLtJ (NOD) + + + age + 8 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801120 + SAMN13527344 + GSM4213200 + + + + + + + SRR10662107 + GSM4213200_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_8w_2849_S2_L001_I1_001.fastq.gz --read2PairFiles=NOD_8w_2849_S2_L001_R1_001.fastq.gz --read3PairFiles=NOD_8w_2849_S2_L001_R2_001.fastq.gz + + + + + + SRS5801120 + SAMN13527344 + GSM4213200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662108 + GSM4213200_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_8w_2849_S2_L002_I1_001.fastq.gz --read2PairFiles=NOD_8w_2849_S2_L002_R1_001.fastq.gz --read3PairFiles=NOD_8w_2849_S2_L002_R2_001.fastq.gz + + + + + + SRS5801120 + SAMN13527344 + GSM4213200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341049 + + GSM4213199: NOD_4_wks_2; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801117 + GSM4213199 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213199 + + + + + + + GEO Accession + GSM4213199 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801117 + SAMN13527345 + GSM4213199 + + NOD_4_wks_2 + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD/ShiLtJ (NOD) + + + age + 4 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801117 + SAMN13527345 + GSM4213199 + + + + + + + SRR10662105 + GSM4213199_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_4w_2849_S5_L001_I1_001.fastq.gz --read2PairFiles=NOD_4w_2849_S5_L001_R1_001.fastq.gz --read3PairFiles=NOD_4w_2849_S5_L001_R2_001.fastq.gz + + + + + + SRS5801117 + SAMN13527345 + GSM4213199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662106 + GSM4213199_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_4w_2849_S5_L002_I1_001.fastq.gz --read2PairFiles=NOD_4w_2849_S5_L002_R1_001.fastq.gz --read3PairFiles=NOD_4w_2849_S5_L002_R2_001.fastq.gz + + + + + + SRS5801117 + SAMN13527345 + GSM4213199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341048 + + GSM4213198: NOD_15_wks; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801119 + GSM4213198 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213198 + + + + + + + GEO Accession + GSM4213198 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801119 + SAMN13527346 + GSM4213198 + + NOD_15_wks + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD/ShiLtJ (NOD) + + + age + 15 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801119 + SAMN13527346 + GSM4213198 + + + + + + + SRR10662103 + GSM4213198_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD15w_2734_S2_L001_I1_001.fastq.gz --read2PairFiles=NOD15w_2734_S2_L001_R1_001.fastq.gz --read3PairFiles=NOD15w_2734_S2_L001_R2_001.fastq.gz + + + + + + SRS5801119 + SAMN13527346 + GSM4213198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662104 + GSM4213198_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD15w_2734_S2_L002_I1_001.fastq.gz --read2PairFiles=NOD15w_2734_S2_L002_R1_001.fastq.gz --read3PairFiles=NOD15w_2734_S2_L002_R2_001.fastq.gz + + + + + + SRS5801119 + SAMN13527346 + GSM4213198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341047 + + GSM4213197: NOD_8_wks_1; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801118 + GSM4213197 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213197 + + + + + + + GEO Accession + GSM4213197 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801118 + SAMN13527347 + GSM4213197 + + NOD_8_wks_1 + + 10090 + Mus musculus + + + + + bioproject + 594724 + + + + + + + source_name + Pancreatic islets + + + strain/background + NOD/ShiLtJ (NOD) + + + age + 8 weeks + + + Sex + female + + + cell type + Pancreatic islet-infiltrating cells + + + + + + + SRS5801118 + SAMN13527347 + GSM4213197 + + + + + + + SRR10662101 + GSM4213197_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_8w_2734_S1_L001_I1_001.fastq.gz --read2PairFiles=NOD_8w_2734_S1_L001_R1_001.fastq.gz --read3PairFiles=NOD_8w_2734_S1_L001_R2_001.fastq.gz + + + + + + SRS5801118 + SAMN13527347 + GSM4213197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662102 + GSM4213197_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_8w_2734_S1_L002_I1_001.fastq.gz --read2PairFiles=NOD_8w_2734_S1_L002_R1_001.fastq.gz --read3PairFiles=NOD_8w_2734_S1_L002_R2_001.fastq.gz + + + + + + SRS5801118 + SAMN13527347 + GSM4213197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX7341046 + + GSM4213196: NOD_4_wks_1; Mus musculus; RNA-Seq + + + SRP235598 + + + + + + + SRS5801116 + GSM4213196 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics). Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit following the manufacturer's protocol. 10X Single Cell 3' v2. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304213196 + + + + + + + GEO Accession + GSM4213196 + + + + + + SRA1009823 + GEO: GSE141784 + + + + NCBI + + + Geo + Curators + + + + + + SRP235598 + PRJNA594724 + GSE141784 + + + Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes + + Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions. Overall design: 10X Single-cell RNASeq + GSE141784 + + + + + pubmed + 32251514 + + + + + + parent_bioproject + PRJNA594719 + + + + + + SRS5801116 + SAMN13527348 + GSM4213196 + + GEO accession GSM4213196 is currently private and is scheduled to be released on Feb 01, 2021. + + 10090 + Mus musculus + + + + + + SRS5801116 + SAMN13527348 + GSM4213196 + + + + + + + SRR10662099 + GSM4213196_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_4w_2734_S3_L001_I1_001.fastq.gz --read2PairFiles=NOD_4w_2734_S3_L001_R1_001.fastq.gz --read3PairFiles=NOD_4w_2734_S3_L001_R2_001.fastq.gz + + + + + + SRS5801116 + SAMN13527348 + GSM4213196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR10662100 + GSM4213196_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TTB --read1PairFiles=NOD_4w_2734_S3_L002_I1_001.fastq.gz --read2PairFiles=NOD_4w_2734_S3_L002_R1_001.fastq.gz --read3PairFiles=NOD_4w_2734_S3_L002_R2_001.fastq.gz + + + + + + SRS5801116 + SAMN13527348 + GSM4213196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE157985.xml b/tests/data/GSE157985.xml new file mode 100644 index 0000000..7c43e1d --- /dev/null +++ b/tests/data/GSE157985.xml @@ -0,0 +1,1604 @@ + + + + + + + SRX9125399 + + GSM4783653: AD_GKO; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368047 + GSM4783653 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783653 + + + + + + + GEO Accession + GSM4783653 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368047 + SAMN16140337 + GSM4783653 + + AD_GKO + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 6 month + + + genotype + J20;GSAP -/- + + + strain + C57BL/6 + + + + + + + SRS7368047 + SAMN16140337 + GSM4783653 + + + + + + + SRR12643480 + GSM4783653_r1 + + + + + + SRS7368047 + SAMN16140337 + GSM4783653 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125398 + + GSM4783652: AD_WT; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368046 + GSM4783652 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783652 + + + + + + + GEO Accession + GSM4783652 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368046 + SAMN16140339 + GSM4783652 + + AD_WT + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 6 month + + + genotype + J20;wild type + + + strain + C57BL/6 + + + + + + + SRS7368046 + SAMN16140339 + GSM4783652 + + + + + + + SRR12643479 + GSM4783652_r1 + + + + + + SRS7368046 + SAMN16140339 + GSM4783652 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125397 + + GSM4783651: GKO_3; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368043 + GSM4783651 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783651 + + + + + + + GEO Accession + GSM4783651 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368043 + SAMN16140341 + GSM4783651 + + GKO_3 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + GSAP -/- + + + strain + C57BL/6 + + + + + + + SRS7368043 + SAMN16140341 + GSM4783651 + + + + + + + SRR12643478 + GSM4783651_r1 + + + + + + SRS7368043 + SAMN16140341 + GSM4783651 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125396 + + GSM4783650: GKO_2; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368042 + GSM4783650 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783650 + + + + + + + GEO Accession + GSM4783650 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368042 + SAMN16140342 + GSM4783650 + + GKO_2 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + GSAP -/- + + + strain + C57BL/6 + + + + + + + SRS7368042 + SAMN16140342 + GSM4783650 + + + + + + + SRR12643477 + GSM4783650_r1 + + + + + + SRS7368042 + SAMN16140342 + GSM4783650 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125395 + + GSM4783649: GKO_1; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368044 + GSM4783649 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783649 + + + + + + + GEO Accession + GSM4783649 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368044 + SAMN16140344 + GSM4783649 + + GKO_1 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + GSAP -/- + + + strain + C57BL/6 + + + + + + + SRS7368044 + SAMN16140344 + GSM4783649 + + + + + + + SRR12643476 + GSM4783649_r1 + + + + + + SRS7368044 + SAMN16140344 + GSM4783649 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125394 + + GSM4783648: WT_3; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368045 + GSM4783648 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783648 + + + + + + + GEO Accession + GSM4783648 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368045 + SAMN16140345 + GSM4783648 + + WT_3 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + wild type + + + strain + C57BL/6 + + + + + + + SRS7368045 + SAMN16140345 + GSM4783648 + + + + + + + SRR12643475 + GSM4783648_r1 + + + + + + SRS7368045 + SAMN16140345 + GSM4783648 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125393 + + GSM4783647: WT_2; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368041 + GSM4783647 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783647 + + + + + + + GEO Accession + GSM4783647 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368041 + SAMN16140306 + GSM4783647 + + WT_2 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + wild type + + + strain + C57BL/6 + + + + + + + SRS7368041 + SAMN16140306 + GSM4783647 + + + + + + + SRR12643474 + GSM4783647_r1 + + + + + + SRS7368041 + SAMN16140306 + GSM4783647 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX9125392 + + GSM4783646: WT_1; Mus musculus; RNA-Seq + + + SRP282467 + + + + + + + SRS7368040 + GSM4783646 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304783646 + + + + + + + GEO Accession + GSM4783646 + + + + + + SRA1125811 + GEO: GSE157985 + + + + NCBI + + + Geo + Curators + + + + + + SRP282467 + PRJNA663585 + GSE157985 + + + GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer's disease + + Gamma-secretase activating protein (GSAP) plays an important role in regulating gamma-secretase activity and specificity, which contributes to the pathogenesis of Alzheimer's disease (AD) and Down syndrome. GSAP is expressed in a variety of cell types in the bain. To elucidate the molecular function of GSAP across different cell types in the brain, we performed single nuclei RNA sequencing (sn-RNAseq) on hippocampal tissues obtained from wildtype (WT) and GSAP knockout (GKO) mice. To further investigate the pathogenic function of GSAP in the AD progression, we also determined effects of GSAP gene deletion in the J20 AD mouse model through sn-RNAseq on hippocampal tissues obtained from J20;WT and J20;GKO mice. Overall design: Single nuclei RNA sequencing was performed using hippocampal tissues from WT (7-month old; 3 mice), GKO (7-month old; 3 mice), J20;WT (6-month old; 1 mouse), and J20;GKO mice (6-month old; 1 mouse). + GSE157985 + + + + + pubmed + 34156424 + + + + + + + SRS7368040 + SAMN16140310 + GSM4783646 + + WT_1 + + 10090 + Mus musculus + + + + + bioproject + 663585 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + age + 7 month + + + genotype + wild type + + + strain + C57BL/6 + + + + + + + SRS7368040 + SAMN16140310 + GSM4783646 + + + + + + + SRR12643473 + GSM4783646_r1 + + + + + + SRS7368040 + SAMN16140310 + GSM4783646 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE163314.xml b/tests/data/GSE163314.xml new file mode 100644 index 0000000..32d2bb3 --- /dev/null +++ b/tests/data/GSE163314.xml @@ -0,0 +1,11508 @@ + + + + + + + SRX9690257 + + GSM4977007: Patient 33 Blood; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887406 + GSM4977007 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304977007 + + + + + + + GEO Accession + GSM4977007 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887406 + SAMN17089946 + GSM4977007 + + Patient 33 Blood + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Periperhal Blood + + + disease state + Co-morbid Crohn's and Spondyloarthritis + + + + + + + SRS7887406 + SAMN17089946 + GSM4977007 + + + + + + + SRR13259640 + GSM4977007_r1 + + + + + + SRS7887406 + SAMN17089946 + GSM4977007 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690256 + + GSM4977006: Patient 33 Colon; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887405 + GSM4977006 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304977006 + + + + + + + GEO Accession + GSM4977006 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887405 + SAMN17089947 + GSM4977006 + + Patient 33 Colon + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Retrosigmoid Colon + + + disease state + Co-morbid Crohn's and Spondyloarthritis + + + + + + + SRS7887405 + SAMN17089947 + GSM4977006 + + + + + + + SRR13259624 + GSM4977006_r1 + + + + + + SRS7887405 + SAMN17089947 + GSM4977006 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690248 + + GSM4976998: Patient 7 Colon; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887397 + GSM4976998 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976998 + + + + + + + GEO Accession + GSM4976998 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887397 + SAMN17089955 + GSM4976998 + + Patient 7 Colon + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Retrosigmoid Colon + + + disease state + Crohn's Disease + + + + + + + SRS7887397 + SAMN17089955 + GSM4976998 + + + + + + + SRR13259520 + GSM4976998_r1 + + + + + + SRS7887397 + SAMN17089955 + GSM4976998 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690246 + + GSM4976996: Patient 5 Colon; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887395 + GSM4976996 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976996 + + + + + + + GEO Accession + GSM4976996 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887395 + SAMN17089957 + GSM4976996 + + Patient 5 Colon + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Retrosigmoid Colon + + + disease state + Healthy Control + + + + + + + SRS7887395 + SAMN17089957 + GSM4976996 + + + + + + + SRR13259512 + GSM4976996_r1 + + + + + + SRS7887395 + SAMN17089957 + GSM4976996 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690245 + + GSM4976995: Patient 3 Blood; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887394 + GSM4976995 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976995 + + + + + + + GEO Accession + GSM4976995 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887394 + SAMN17089959 + GSM4976995 + + Patient 3 Blood + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Periperhal Blood + + + disease state + Spondyloarhtritis + + + + + + + SRS7887394 + SAMN17089959 + GSM4976995 + + + + + + + SRR13259508 + GSM4976995_r1 + + + + + + SRS7887394 + SAMN17089959 + GSM4976995 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690244 + + GSM4976994: Patient 3 Colon; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887393 + GSM4976994 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976994 + + + + + + + GEO Accession + GSM4976994 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887393 + SAMN17089960 + GSM4976994 + + Patient 3 Colon + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Retrosigmoid Colon + + + disease state + Spondyloarhtritis + + + + + + + SRS7887393 + SAMN17089960 + GSM4976994 + + + + + + + SRR13259664 + GSM4976994_r1 + + + + + + SRS7887393 + SAMN17089960 + GSM4976994 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690243 + + GSM4976993: Patient 2 Blood; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887392 + GSM4976993 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976993 + + + + + + + GEO Accession + GSM4976993 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887392 + SAMN17089961 + GSM4976993 + + Patient 2 Blood + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Periperhal Blood + + + disease state + Co-morbid Crohn's and Spondyloarthritis + + + + + + + SRS7887392 + SAMN17089961 + GSM4976993 + + + + + + + SRR13259660 + GSM4976993_r1 + + + + + + SRS7887392 + SAMN17089961 + GSM4976993 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX9690242 + + GSM4976992: Patient 2 Colon; Homo sapiens; RNA-Seq + + + SRP298136 + + + + + + + SRS7887391 + GSM4976992 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 304976992 + + + + + + + GEO Accession + GSM4976992 + + + + + + SRA1174324 + GEO: GSE163314 + + + + NCBI + + + Geo + Curators + + + + + + SRP298136 + PRJNA685745 + GSE163314 + + + Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases + + This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects. Overall design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue + GSE163314 + + + + + pubmed + 34022940 + + + + + + + SRS7887391 + SAMN17089962 + GSM4976992 + + Patient 2 Colon + + 9606 + Homo sapiens + + + + + bioproject + 685745 + + + + + + + source_name + Retrosigmoid Colon + + + disease state + Co-morbid Crohn's and Spondyloarthritis + + + + + + + SRS7887391 + SAMN17089962 + GSM4976992 + + + + + + + SRR13259656 + GSM4976992_r1 + + + + + + SRS7887391 + SAMN17089962 + GSM4976992 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR13259659 + GSM4976992_r4 + + + + + + SRS7887391 + SAMN17089962 + GSM4976992 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE173242.xml b/tests/data/GSE173242.xml new file mode 100644 index 0000000..dcadad8 --- /dev/null +++ b/tests/data/GSE173242.xml @@ -0,0 +1,1930 @@ + + + + + + + SRX10674721 + + GSM5264252: SP064_030: APPPS1 snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768723 + GSM5264252 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264252 + + + + + + + GEO Accession + GSM5264252 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768723 + SAMN18863727 + GSM5264252 + + SP064_030: APPPS1 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P + + + + + + + SRS8768723 + SAMN18863727 + GSM5264252 + + + + + + + SRR14319573 + GSM5264252_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_030_S9_I1_001.fastq.gz --read2PairFiles=SP064_030_S9_R1_001.fastq.gz --read3PairFiles=SP064_030_S9_R2_001.fastq.gz + + + + + + SRS8768723 + SAMN18863727 + GSM5264252 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674720 + + GSM5264251: SP064_029: APPPS1.p40KO snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768722 + GSM5264251 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264251 + + + + + + + GEO Accession + GSM5264251 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768722 + SAMN18863728 + GSM5264251 + + SP064_029: APPPS1.p40KO snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-4 + + + + + + + SRS8768722 + SAMN18863728 + GSM5264251 + + + + + + + SRR14319572 + GSM5264251_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_029_S8_I1_001.fastq.gz --read2PairFiles=SP064_029_S8_R1_001.fastq.gz --read3PairFiles=SP064_029_S8_R2_001.fastq.gz + + + + + + SRS8768722 + SAMN18863728 + GSM5264251 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674719 + + GSM5264250: SP064_028: WT snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768721 + GSM5264250 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264250 + + + + + + + GEO Accession + GSM5264250 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768721 + SAMN18863729 + GSM5264250 + + SP064_028: WT snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + none + + + + + + + SRS8768721 + SAMN18863729 + GSM5264250 + + + + + + + SRR14319571 + GSM5264250_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_028_S7_I1_001.fastq.gz --read2PairFiles=SP064_028_S7_R1_001.fastq.gz --read3PairFiles=SP064_028_S7_R2_001.fastq.gz + + + + + + SRS8768721 + SAMN18863729 + GSM5264250 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674718 + + GSM5264249: SP064_027: APPPS1 snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768720 + GSM5264249 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264249 + + + + + + + GEO Accession + GSM5264249 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768720 + SAMN18863731 + GSM5264249 + + SP064_027: APPPS1 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P + + + + + + + SRS8768720 + SAMN18863731 + GSM5264249 + + + + + + + SRR14319570 + GSM5264249_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_027_S6_I1_001.fastq.gz --read2PairFiles=SP064_027_S6_R1_001.fastq.gz --read3PairFiles=SP064_027_S6_R2_001.fastq.gz + + + + + + SRS8768720 + SAMN18863731 + GSM5264249 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674717 + + GSM5264248: SP064_026: APPPS1.p40KO snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768719 + GSM5264248 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264248 + + + + + + + GEO Accession + GSM5264248 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768719 + SAMN18863732 + GSM5264248 + + SP064_026: APPPS1.p40KO snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-3 + + + + + + + SRS8768719 + SAMN18863732 + GSM5264248 + + + + + + + SRR14319569 + GSM5264248_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_026_S5_I1_001.fastq.gz --read2PairFiles=SP064_026_S5_R1_001.fastq.gz --read3PairFiles=SP064_026_S5_R2_001.fastq.gz + + + + + + SRS8768719 + SAMN18863732 + GSM5264248 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674716 + + GSM5264247: SP064_025: WT snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768718 + GSM5264247 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264247 + + + + + + + GEO Accession + GSM5264247 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768718 + SAMN18863734 + GSM5264247 + + SP064_025: WT snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + none + + + + + + + SRS8768718 + SAMN18863734 + GSM5264247 + + + + + + + SRR14319568 + GSM5264247_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_025_S4_I1_001.fastq.gz --read2PairFiles=SP064_025_S4_R1_001.fastq.gz --read3PairFiles=SP064_025_S4_R2_001.fastq.gz + + + + + + SRS8768718 + SAMN18863734 + GSM5264247 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674715 + + GSM5264246: SP064_024: APPPS1 snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768717 + GSM5264246 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264246 + + + + + + + GEO Accession + GSM5264246 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768717 + SAMN18863735 + GSM5264246 + + SP064_024: APPPS1 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P + + + + + + + SRS8768717 + SAMN18863735 + GSM5264246 + + + + + + + SRR14319567 + GSM5264246_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_024_S3_I1_001.fastq.gz --read2PairFiles=SP064_024_S3_R1_001.fastq.gz --read3PairFiles=SP064_024_S3_R2_001.fastq.gz + + + + + + SRS8768717 + SAMN18863735 + GSM5264246 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674714 + + GSM5264245: SP064_023: APPPS1.p40KO snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768716 + GSM5264245 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264245 + + + + + + + GEO Accession + GSM5264245 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768716 + SAMN18863736 + GSM5264245 + + SP064_023: APPPS1.p40KO snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + APP KM670/671NL (Swedish), PSEN1 L166P, Il12b knock out exon 1-2 + + + + + + + SRS8768716 + SAMN18863736 + GSM5264245 + + + + + + + SRR14319566 + GSM5264245_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_023_S2_I1_001.fastq.gz --read2PairFiles=SP064_023_S2_R1_001.fastq.gz --read3PairFiles=SP064_023_S2_R2_001.fastq.gz + + + + + + SRS8768716 + SAMN18863736 + GSM5264245 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10674713 + + GSM5264244: SP064_022: WT snRNA-seq; Mus musculus; RNA-Seq + + + SRP316186 + + + + + + + SRS8768715 + GSM5264244 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Hippocampus prepped and immediately flash frozen. Nuclei extracted using mechanical and lysis buffer. Isolated nuclei stained with DAPI and subjected to FACS. 10 000 cells/sample utilized for downstream single-nuclei barcoding using for droplet-based 3′end single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ GEM According to manufacturer recommendation of Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305264244 + + + + + + + GEO Accession + GSM5264244 + + + + + + SRA1223253 + GEO: GSE173242 + + + + NCBI + + + Geo + Curators + + + + + + SRP316186 + PRJNA724867 + GSE173242 + + + The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis + + Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. Overall design: Single-nuclei RNAseq of FACs sorted nuclei extracted from snap frozen mouse hippocampus of 250 day old animals + GSE173242 + + + + + pubmed + 40082619 + + + + + + + SRS8768715 + SAMN18863737 + GSM5264244 + + SP064_022: WT snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 724867 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + 250 day + + + strain + C57BL/6J + + + mutation + none + + + + + + + SRS8768715 + SAMN18863737 + GSM5264244 + + + + + + + SRR14319565 + GSM5264244_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=SP064_022_S1_I1_001.fastq.gz --read2PairFiles=SP064_022_S1_R1_001.fastq.gz --read3PairFiles=SP064_022_S1_R2_001.fastq.gz + + + + + + SRS8768715 + SAMN18863737 + GSM5264244 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE174332.xml b/tests/data/GSE174332.xml new file mode 100644 index 0000000..4f37cf7 --- /dev/null +++ b/tests/data/GSE174332.xml @@ -0,0 +1,18154 @@ + + + + + + + SRX10857454 + + GSM5292208: 201025_FTLD_240_snRNA-C12; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952935 + GSM5292208 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292208 + + + + + + + GEO Accession + GSM5292208 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952935 + SAMN19117464 + GSM5292208 + + 201025_FTLD_240_snRNA-C12 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 240 + + + disease state + c9FTLD + + + + + + + SRS8952935 + SAMN19117464 + GSM5292208 + + + + + + + SRR14511706 + GSM5292208_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_240_snRNA-C12_S16_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_240_snRNA-C12_S16_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_240_snRNA-C12_S16_L001_I1_001.fastq.gz + + + + + + SRS8952935 + SAMN19117464 + GSM5292208 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511707 + GSM5292208_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_240_snRNA-C12_S16_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_240_snRNA-C12_S16_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_240_snRNA-C12_S16_L002_I1_001.fastq.gz + + + + + + SRS8952935 + SAMN19117464 + GSM5292208 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857453 + + GSM5292207: 201025_FTLD_239_snRNA-C11; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952934 + GSM5292207 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292207 + + + + + + + GEO Accession + GSM5292207 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952934 + SAMN19117465 + GSM5292207 + + 201025_FTLD_239_snRNA-C11 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 239 + + + disease state + c9FTLD + + + + + + + SRS8952934 + SAMN19117465 + GSM5292207 + + + + + + + SRR14511704 + GSM5292207_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_239_snRNA-C11_S15_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_239_snRNA-C11_S15_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_239_snRNA-C11_S15_L001_I1_001.fastq.gz + + + + + + SRS8952934 + SAMN19117465 + GSM5292207 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511705 + GSM5292207_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_239_snRNA-C11_S15_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_239_snRNA-C11_S15_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_239_snRNA-C11_S15_L002_I1_001.fastq.gz + + + + + + SRS8952934 + SAMN19117465 + GSM5292207 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857452 + + GSM5292206: 201025_FTLD_238_snRNA-C10; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952933 + GSM5292206 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292206 + + + + + + + GEO Accession + GSM5292206 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952933 + SAMN19117496 + GSM5292206 + + 201025_FTLD_238_snRNA-C10 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 238 + + + disease state + c9FTLD + + + + + + + SRS8952933 + SAMN19117496 + GSM5292206 + + + + + + + SRR14511702 + GSM5292206_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_238_snRNA-C10_S14_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_238_snRNA-C10_S14_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_238_snRNA-C10_S14_L001_I1_001.fastq.gz + + + + + + SRS8952933 + SAMN19117496 + GSM5292206 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511703 + GSM5292206_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_238_snRNA-C10_S14_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_238_snRNA-C10_S14_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_238_snRNA-C10_S14_L002_I1_001.fastq.gz + + + + + + SRS8952933 + SAMN19117496 + GSM5292206 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857451 + + GSM5292205: 201025_FTLD_237_snRNA-C9; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952932 + GSM5292205 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292205 + + + + + + + GEO Accession + GSM5292205 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952932 + SAMN19117432 + GSM5292205 + + 201025_FTLD_237_snRNA-C9 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 237 + + + disease state + c9FTLD + + + + + + + SRS8952932 + SAMN19117432 + GSM5292205 + + + + + + + SRR14511700 + GSM5292205_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_237_snRNA-C9_S13_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_237_snRNA-C9_S13_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_237_snRNA-C9_S13_L001_I1_001.fastq.gz + + + + + + SRS8952932 + SAMN19117432 + GSM5292205 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511701 + GSM5292205_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_237_snRNA-C9_S13_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_237_snRNA-C9_S13_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_237_snRNA-C9_S13_L002_I1_001.fastq.gz + + + + + + SRS8952932 + SAMN19117432 + GSM5292205 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857450 + + GSM5292204: 201025_FTLD_235_snRNA-C7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952931 + GSM5292204 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292204 + + + + + + + GEO Accession + GSM5292204 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952931 + SAMN19117433 + GSM5292204 + + 201025_FTLD_235_snRNA-C7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 235 + + + disease state + c9FTLD + + + + + + + SRS8952931 + SAMN19117433 + GSM5292204 + + + + + + + SRR14511698 + GSM5292204_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_235_snRNA-C7_S11_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_235_snRNA-C7_S11_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_235_snRNA-C7_S11_L001_I1_001.fastq.gz + + + + + + SRS8952931 + SAMN19117433 + GSM5292204 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511699 + GSM5292204_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_235_snRNA-C7_S11_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_235_snRNA-C7_S11_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_235_snRNA-C7_S11_L002_I1_001.fastq.gz + + + + + + SRS8952931 + SAMN19117433 + GSM5292204 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857449 + + GSM5292203: 201025_FTLD_234_snRNA-C6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952930 + GSM5292203 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292203 + + + + + + + GEO Accession + GSM5292203 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952930 + SAMN19117463 + GSM5292203 + + 201025_FTLD_234_snRNA-C6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 234 + + + disease state + c9FTLD + + + + + + + SRS8952930 + SAMN19117463 + GSM5292203 + + + + + + + SRR14511696 + GSM5292203_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_234_snRNA-C6_S10_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_234_snRNA-C6_S10_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_234_snRNA-C6_S10_L001_I1_001.fastq.gz + + + + + + SRS8952930 + SAMN19117463 + GSM5292203 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511697 + GSM5292203_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_234_snRNA-C6_S10_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_234_snRNA-C6_S10_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_234_snRNA-C6_S10_L002_I1_001.fastq.gz + + + + + + SRS8952930 + SAMN19117463 + GSM5292203 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857448 + + GSM5292202: 201025_FTLD_232_snRNA-C5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952929 + GSM5292202 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292202 + + + + + + + GEO Accession + GSM5292202 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952929 + SAMN19117466 + GSM5292202 + + 201025_FTLD_232_snRNA-C5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 232 + + + disease state + c9FTLD + + + + + + + SRS8952929 + SAMN19117466 + GSM5292202 + + + + + + + SRR14511694 + GSM5292202_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_232_snRNA-C5_S9_L001_R1_001.fastq.gz --read2PairFiles=201025_FTLD_232_snRNA-C5_S9_L001_R2_001.fastq.gz --read3PairFiles=201025_FTLD_232_snRNA-C5_S9_L001_I1_001.fastq.gz + + + + + + SRS8952929 + SAMN19117466 + GSM5292202 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511695 + GSM5292202_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201025_FTLD_232_snRNA-C5_S9_L002_R1_001.fastq.gz --read2PairFiles=201025_FTLD_232_snRNA-C5_S9_L002_R2_001.fastq.gz --read3PairFiles=201025_FTLD_232_snRNA-C5_S9_L002_I1_001.fastq.gz + + + + + + SRS8952929 + SAMN19117466 + GSM5292202 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857447 + + GSM5292201: 201019_PN_311_snRNA-B8; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952928 + GSM5292201 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292201 + + + + + + + GEO Accession + GSM5292201 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952928 + SAMN19117467 + GSM5292201 + + 201019_PN_311_snRNA-B8 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 311 + + + disease state + PN + + + + + + + SRS8952928 + SAMN19117467 + GSM5292201 + + + + + + + SRR14511692 + GSM5292201_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_PN_311_snRNA-B8_S8_L001_R1_001.fastq.gz --read2PairFiles=201019_PN_311_snRNA-B8_S8_L001_R2_001.fastq.gz --read3PairFiles=201019_PN_311_snRNA-B8_S8_L001_I1_001.fastq.gz + + + + + + SRS8952928 + SAMN19117467 + GSM5292201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511693 + GSM5292201_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_PN_311_snRNA-B8_S8_L002_R1_001.fastq.gz --read2PairFiles=201019_PN_311_snRNA-B8_S8_L002_R2_001.fastq.gz --read3PairFiles=201019_PN_311_snRNA-B8_S8_L002_I1_001.fastq.gz + + + + + + SRS8952928 + SAMN19117467 + GSM5292201 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857446 + + GSM5292200: 201019_ALS_113_snRNA-B7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952927 + GSM5292200 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292200 + + + + + + + GEO Accession + GSM5292200 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952927 + SAMN19117468 + GSM5292200 + + 201019_ALS_113_snRNA-B7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 113 + + + disease state + c9ALS + + + + + + + SRS8952927 + SAMN19117468 + GSM5292200 + + + + + + + SRR14511690 + GSM5292200_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_113_snRNA-B7_S7_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_113_snRNA-B7_S7_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_113_snRNA-B7_S7_L001_I1_001.fastq.gz + + + + + + SRS8952927 + SAMN19117468 + GSM5292200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511691 + GSM5292200_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_113_snRNA-B7_S7_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_113_snRNA-B7_S7_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_113_snRNA-B7_S7_L002_I1_001.fastq.gz + + + + + + SRS8952927 + SAMN19117468 + GSM5292200 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857445 + + GSM5292199: 201019_ALS_108_snRNA-B6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952926 + GSM5292199 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292199 + + + + + + + GEO Accession + GSM5292199 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952926 + SAMN19117497 + GSM5292199 + + 201019_ALS_108_snRNA-B6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 108 + + + disease state + sALS + + + + + + + SRS8952926 + SAMN19117497 + GSM5292199 + + + + + + + SRR14511688 + GSM5292199_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_108_snRNA-B6_S6_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_108_snRNA-B6_S6_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_108_snRNA-B6_S6_L001_I1_001.fastq.gz + + + + + + SRS8952926 + SAMN19117497 + GSM5292199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511689 + GSM5292199_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_108_snRNA-B6_S6_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_108_snRNA-B6_S6_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_108_snRNA-B6_S6_L002_I1_001.fastq.gz + + + + + + SRS8952926 + SAMN19117497 + GSM5292199 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857444 + + GSM5292198: 201019_ALS_106_snRNA-B5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952925 + GSM5292198 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292198 + + + + + + + GEO Accession + GSM5292198 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952925 + SAMN19117430 + GSM5292198 + + 201019_ALS_106_snRNA-B5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 106 + + + disease state + sALS + + + + + + + SRS8952925 + SAMN19117430 + GSM5292198 + + + + + + + SRR14511686 + GSM5292198_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_106_snRNA-B5_S5_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_106_snRNA-B5_S5_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_106_snRNA-B5_S5_L001_I1_001.fastq.gz + + + + + + SRS8952925 + SAMN19117430 + GSM5292198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511687 + GSM5292198_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_106_snRNA-B5_S5_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_106_snRNA-B5_S5_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_106_snRNA-B5_S5_L002_I1_001.fastq.gz + + + + + + SRS8952925 + SAMN19117430 + GSM5292198 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857443 + + GSM5292197: 201019_ALS_104_snRNA-B4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952924 + GSM5292197 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292197 + + + + + + + GEO Accession + GSM5292197 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952924 + SAMN19117431 + GSM5292197 + + 201019_ALS_104_snRNA-B4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 104 + + + disease state + sALS + + + + + + + SRS8952924 + SAMN19117431 + GSM5292197 + + + + + + + SRR14511684 + GSM5292197_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_104_snRNA-B4_S4_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_104_snRNA-B4_S4_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_104_snRNA-B4_S4_L001_I1_001.fastq.gz + + + + + + SRS8952924 + SAMN19117431 + GSM5292197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511685 + GSM5292197_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_104_snRNA-B4_S4_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_104_snRNA-B4_S4_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_104_snRNA-B4_S4_L002_I1_001.fastq.gz + + + + + + SRS8952924 + SAMN19117431 + GSM5292197 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857442 + + GSM5292196: 201019_ALS_103_snRNA-B3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8953072 + GSM5292196 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292196 + + + + + + + GEO Accession + GSM5292196 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8953072 + SAMN19117469 + GSM5292196 + + 201019_ALS_103_snRNA-B3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 103 + + + disease state + sALS + + + + + + + SRS8953072 + SAMN19117469 + GSM5292196 + + + + + + + SRR14511682 + GSM5292196_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_103_snRNA-B3_S3_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_103_snRNA-B3_S3_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_103_snRNA-B3_S3_L001_I1_001.fastq.gz + + + + + + SRS8953072 + SAMN19117469 + GSM5292196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511683 + GSM5292196_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_103_snRNA-B3_S3_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_103_snRNA-B3_S3_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_103_snRNA-B3_S3_L002_I1_001.fastq.gz + + + + + + SRS8953072 + SAMN19117469 + GSM5292196 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857441 + + GSM5292195: 201019_ALS_102_snRNA-B2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952923 + GSM5292195 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292195 + + + + + + + GEO Accession + GSM5292195 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952923 + SAMN19117470 + GSM5292195 + + 201019_ALS_102_snRNA-B2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 102 + + + disease state + sALS + + + + + + + SRS8952923 + SAMN19117470 + GSM5292195 + + + + + + + SRR14511680 + GSM5292195_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_102_snRNA-B2_S2_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_102_snRNA-B2_S2_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_102_snRNA-B2_S2_L001_I1_001.fastq.gz + + + + + + SRS8952923 + SAMN19117470 + GSM5292195 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511681 + GSM5292195_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_102_snRNA-B2_S2_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_102_snRNA-B2_S2_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_102_snRNA-B2_S2_L002_I1_001.fastq.gz + + + + + + SRS8952923 + SAMN19117470 + GSM5292195 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857440 + + GSM5292194: 201019_ALS_101_snRNA-B1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952922 + GSM5292194 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292194 + + + + + + + GEO Accession + GSM5292194 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952922 + SAMN19117471 + GSM5292194 + + 201019_ALS_101_snRNA-B1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 101 + + + disease state + sALS + + + + + + + SRS8952922 + SAMN19117471 + GSM5292194 + + + + + + + SRR14511678 + GSM5292194_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_101_snRNA-B1_S1_L001_R1_001.fastq.gz --read2PairFiles=201019_ALS_101_snRNA-B1_S1_L001_R2_001.fastq.gz --read3PairFiles=201019_ALS_101_snRNA-B1_S1_L001_I1_001.fastq.gz + + + + + + SRS8952922 + SAMN19117471 + GSM5292194 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511679 + GSM5292194_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=201019_ALS_101_snRNA-B1_S1_L002_R1_001.fastq.gz --read2PairFiles=201019_ALS_101_snRNA-B1_S1_L002_R2_001.fastq.gz --read3PairFiles=201019_ALS_101_snRNA-B1_S1_L002_I1_001.fastq.gz + + + + + + SRS8952922 + SAMN19117471 + GSM5292194 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857439 + + GSM5292193: 200721_PN_302_snRNA-B4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952921 + GSM5292193 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292193 + + + + + + + GEO Accession + GSM5292193 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952921 + SAMN19117472 + GSM5292193 + + 200721_PN_302_snRNA-B4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 302 + + + disease state + PN + + + + + + + SRS8952921 + SAMN19117472 + GSM5292193 + + + + + + + SRR14511676 + GSM5292193_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_PN_302_snRNA-B4_S7_L001_R1_001.fastq.gz --read2PairFiles=200721_PN_302_snRNA-B4_S7_L001_R2_001.fastq.gz --read3PairFiles=200721_PN_302_snRNA-B4_S7_L001_I1_001.fastq.gz + + + + + + SRS8952921 + SAMN19117472 + GSM5292193 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511677 + GSM5292193_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_PN_302_snRNA-B4_S7_L002_R1_001.fastq.gz --read2PairFiles=200721_PN_302_snRNA-B4_S7_L002_R2_001.fastq.gz --read3PairFiles=200721_PN_302_snRNA-B4_S7_L002_I1_001.fastq.gz + + + + + + SRS8952921 + SAMN19117472 + GSM5292193 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857438 + + GSM5292192: 200721_FTLD_229_snRNA-B2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952920 + GSM5292192 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292192 + + + + + + + GEO Accession + GSM5292192 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952920 + SAMN19117473 + GSM5292192 + + 200721_FTLD_229_snRNA-B2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 229 + + + disease state + c9FTLD + + + + + + + SRS8952920 + SAMN19117473 + GSM5292192 + + + + + + + SRR14511674 + GSM5292192_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_229_snRNA-B2_S5_L001_R1_001.fastq.gz --read2PairFiles=200721_FTLD_229_snRNA-B2_S5_L001_R2_001.fastq.gz --read3PairFiles=200721_FTLD_229_snRNA-B2_S5_L001_I1_001.fastq.gz + + + + + + SRS8952920 + SAMN19117473 + GSM5292192 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511675 + GSM5292192_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_229_snRNA-B2_S5_L002_R1_001.fastq.gz --read2PairFiles=200721_FTLD_229_snRNA-B2_S5_L002_R2_001.fastq.gz --read3PairFiles=200721_FTLD_229_snRNA-B2_S5_L002_I1_001.fastq.gz + + + + + + SRS8952920 + SAMN19117473 + GSM5292192 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857437 + + GSM5292191: 200721_FTLD_214_snRNA-A12; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952919 + GSM5292191 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292191 + + + + + + + GEO Accession + GSM5292191 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952919 + SAMN19117474 + GSM5292191 + + 200721_FTLD_214_snRNA-A12 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 214 + + + disease state + c9FTLD + + + + + + + SRS8952919 + SAMN19117474 + GSM5292191 + + + + + + + SRR14511672 + GSM5292191_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_214_snRNA-A12_S3_L001_R1_001.fastq.gz --read2PairFiles=200721_FTLD_214_snRNA-A12_S3_L001_R2_001.fastq.gz --read3PairFiles=200721_FTLD_214_snRNA-A12_S3_L001_I1_001.fastq.gz + + + + + + SRS8952919 + SAMN19117474 + GSM5292191 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511673 + GSM5292191_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_214_snRNA-A12_S3_L002_R1_001.fastq.gz --read2PairFiles=200721_FTLD_214_snRNA-A12_S3_L002_R2_001.fastq.gz --read3PairFiles=200721_FTLD_214_snRNA-A12_S3_L002_I1_001.fastq.gz + + + + + + SRS8952919 + SAMN19117474 + GSM5292191 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857436 + + GSM5292190: 200721_FTLD_210_snRNA-A11; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952918 + GSM5292190 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292190 + + + + + + + GEO Accession + GSM5292190 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952918 + SAMN19117475 + GSM5292190 + + 200721_FTLD_210_snRNA-A11 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 210 + + + disease state + c9FTLD + + + + + + + SRS8952918 + SAMN19117475 + GSM5292190 + + + + + + + SRR14511670 + GSM5292190_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_210_snRNA-A11_S2_L001_R1_001.fastq.gz --read2PairFiles=200721_FTLD_210_snRNA-A11_S2_L001_R2_001.fastq.gz --read3PairFiles=200721_FTLD_210_snRNA-A11_S2_L001_I1_001.fastq.gz + + + + + + SRS8952918 + SAMN19117475 + GSM5292190 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511671 + GSM5292190_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_210_snRNA-A11_S2_L002_R1_001.fastq.gz --read2PairFiles=200721_FTLD_210_snRNA-A11_S2_L002_R2_001.fastq.gz --read3PairFiles=200721_FTLD_210_snRNA-A11_S2_L002_I1_001.fastq.gz + + + + + + SRS8952918 + SAMN19117475 + GSM5292190 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857435 + + GSM5292189: 200721_FTLD_206_snRNA-A10; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952917 + GSM5292189 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292189 + + + + + + + GEO Accession + GSM5292189 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952917 + SAMN19117476 + GSM5292189 + + 200721_FTLD_206_snRNA-A10 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 206 + + + disease state + sFTLD + + + + + + + SRS8952917 + SAMN19117476 + GSM5292189 + + + + + + + SRR14511668 + GSM5292189_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=200721_FTLD_206_snRNA-A10_S1_L001_R1_001.fastq.gz --read2PairFiles=200721_FTLD_206_snRNA-A10_S1_L001_R2_001.fastq.gz --read3PairFiles=200721_FTLD_206_snRNA-A10_S1_L001_I1_001.fastq.gz + + + + + + SRS8952917 + SAMN19117476 + GSM5292189 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511669 + GSM5292189_r2 + + + + + loader + fastq-load.py + + + options + --doNotUseSharq --allowEarlyFileEnd + + + + + + SRS8952917 + SAMN19117476 + GSM5292189 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857434 + + GSM5292188: 191114_PN_328_snRNA-F9; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952916 + GSM5292188 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292188 + + + + + + + GEO Accession + GSM5292188 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952916 + SAMN19117477 + GSM5292188 + + 191114_PN_328_snRNA-F9 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 328 + + + disease state + PN + + + + + + + SRS8952916 + SAMN19117477 + GSM5292188 + + + + + + + SRR14511666 + GSM5292188_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_328_snRNA-F9_S15_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_328_snRNA-F9_S15_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_328_snRNA-F9_S15_L001_I1_001.fastq.gz + + + + + + SRS8952916 + SAMN19117477 + GSM5292188 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511667 + GSM5292188_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_328_snRNA-F9_S15_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_328_snRNA-F9_S15_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_328_snRNA-F9_S15_L002_I1_001.fastq.gz + + + + + + SRS8952916 + SAMN19117477 + GSM5292188 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857433 + + GSM5292187: 191114_PN_325_snRNA-F8; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952915 + GSM5292187 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292187 + + + + + + + GEO Accession + GSM5292187 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952915 + SAMN19117478 + GSM5292187 + + 191114_PN_325_snRNA-F8 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 325 + + + disease state + PN + + + + + + + SRS8952915 + SAMN19117478 + GSM5292187 + + + + + + + SRR14511664 + GSM5292187_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_325_snRNA-F8_S14_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_325_snRNA-F8_S14_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_325_snRNA-F8_S14_L001_I1_001.fastq.gz + + + + + + SRS8952915 + SAMN19117478 + GSM5292187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511665 + GSM5292187_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_325_snRNA-F8_S14_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_325_snRNA-F8_S14_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_325_snRNA-F8_S14_L002_I1_001.fastq.gz + + + + + + SRS8952915 + SAMN19117478 + GSM5292187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857432 + + GSM5292186: 191114_PN_324_snRNA-F7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952914 + GSM5292186 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292186 + + + + + + + GEO Accession + GSM5292186 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952914 + SAMN19117479 + GSM5292186 + + 191114_PN_324_snRNA-F7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 324 + + + disease state + PN + + + + + + + SRS8952914 + SAMN19117479 + GSM5292186 + + + + + + + SRR14511662 + GSM5292186_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_324_snRNA-F7_S13_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_324_snRNA-F7_S13_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_324_snRNA-F7_S13_L001_I1_001.fastq.gz + + + + + + SRS8952914 + SAMN19117479 + GSM5292186 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511663 + GSM5292186_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_324_snRNA-F7_S13_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_324_snRNA-F7_S13_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_324_snRNA-F7_S13_L002_I1_001.fastq.gz + + + + + + SRS8952914 + SAMN19117479 + GSM5292186 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857431 + + GSM5292185: 191114_PN_323_snRNA-F6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952913 + GSM5292185 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292185 + + + + + + + GEO Accession + GSM5292185 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952913 + SAMN19117480 + GSM5292185 + + 191114_PN_323_snRNA-F6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 323 + + + disease state + PN + + + + + + + SRS8952913 + SAMN19117480 + GSM5292185 + + + + + + + SRR14511660 + GSM5292185_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_323_snRNA-F6_S16_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_323_snRNA-F6_S16_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_323_snRNA-F6_S16_L001_I1_001.fastq.gz + + + + + + SRS8952913 + SAMN19117480 + GSM5292185 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511661 + GSM5292185_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_323_snRNA-F6_S16_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_323_snRNA-F6_S16_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_323_snRNA-F6_S16_L002_I1_001.fastq.gz + + + + + + SRS8952913 + SAMN19117480 + GSM5292185 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857430 + + GSM5292184: 191114_PN_322_snRNA-F5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952912 + GSM5292184 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292184 + + + + + + + GEO Accession + GSM5292184 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952912 + SAMN19117481 + GSM5292184 + + 191114_PN_322_snRNA-F5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 322 + + + disease state + PN + + + + + + + SRS8952912 + SAMN19117481 + GSM5292184 + + + + + + + SRR14511658 + GSM5292184_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_322_snRNA-F5_S15_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_322_snRNA-F5_S15_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_322_snRNA-F5_S15_L001_I1_001.fastq.gz + + + + + + SRS8952912 + SAMN19117481 + GSM5292184 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511659 + GSM5292184_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_322_snRNA-F5_S15_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_322_snRNA-F5_S15_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_322_snRNA-F5_S15_L002_I1_001.fastq.gz + + + + + + SRS8952912 + SAMN19117481 + GSM5292184 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857429 + + GSM5292183: 191114_PN_319_snRNA-F4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952911 + GSM5292183 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292183 + + + + + + + GEO Accession + GSM5292183 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952911 + SAMN19117482 + GSM5292183 + + 191114_PN_319_snRNA-F4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 319 + + + disease state + PN + + + + + + + SRS8952911 + SAMN19117482 + GSM5292183 + + + + + + + SRR14511656 + GSM5292183_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_319_snRNA-F4_S14_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_319_snRNA-F4_S14_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_319_snRNA-F4_S14_L001_I1_001.fastq.gz + + + + + + SRS8952911 + SAMN19117482 + GSM5292183 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511657 + GSM5292183_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_319_snRNA-F4_S14_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_319_snRNA-F4_S14_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_319_snRNA-F4_S14_L002_I1_001.fastq.gz + + + + + + SRS8952911 + SAMN19117482 + GSM5292183 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857428 + + GSM5292182: 191114_PN_318_snRNA-F3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952910 + GSM5292182 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292182 + + + + + + + GEO Accession + GSM5292182 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952910 + SAMN19117483 + GSM5292182 + + 191114_PN_318_snRNA-F3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 318 + + + disease state + PN + + + + + + + SRS8952910 + SAMN19117483 + GSM5292182 + + + + + + + SRR14511654 + GSM5292182_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_318_snRNA-F3_S13_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_318_snRNA-F3_S13_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_318_snRNA-F3_S13_L001_I1_001.fastq.gz + + + + + + SRS8952910 + SAMN19117483 + GSM5292182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511655 + GSM5292182_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_318_snRNA-F3_S13_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_318_snRNA-F3_S13_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_318_snRNA-F3_S13_L002_I1_001.fastq.gz + + + + + + SRS8952910 + SAMN19117483 + GSM5292182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857427 + + GSM5292181: 191114_PN_317_snRNA-F2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952909 + GSM5292181 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292181 + + + + + + + GEO Accession + GSM5292181 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952909 + SAMN19117484 + GSM5292181 + + 191114_PN_317_snRNA-F2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 317 + + + disease state + PN + + + + + + + SRS8952909 + SAMN19117484 + GSM5292181 + + + + + + + SRR14511652 + GSM5292181_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_317_snRNA-F2_S16_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_317_snRNA-F2_S16_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_317_snRNA-F2_S16_L001_I1_001.fastq.gz + + + + + + SRS8952909 + SAMN19117484 + GSM5292181 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511653 + GSM5292181_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_317_snRNA-F2_S16_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_317_snRNA-F2_S16_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_317_snRNA-F2_S16_L002_I1_001.fastq.gz + + + + + + SRS8952909 + SAMN19117484 + GSM5292181 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857426 + + GSM5292180: 191114_PN_309_snRNA-F1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952908 + GSM5292180 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292180 + + + + + + + GEO Accession + GSM5292180 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952908 + SAMN19117485 + GSM5292180 + + 191114_PN_309_snRNA-F1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 309 + + + disease state + PN + + + + + + + SRS8952908 + SAMN19117485 + GSM5292180 + + + + + + + SRR14511650 + GSM5292180_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_309_snRNA-F1_S15_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_309_snRNA-F1_S15_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_309_snRNA-F1_S15_L001_I1_001.fastq.gz + + + + + + SRS8952908 + SAMN19117485 + GSM5292180 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511651 + GSM5292180_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_309_snRNA-F1_S15_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_309_snRNA-F1_S15_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_309_snRNA-F1_S15_L002_I1_001.fastq.gz + + + + + + SRS8952908 + SAMN19117485 + GSM5292180 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857425 + + GSM5292179: 191114_PN_308_snRNA-E12; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952907 + GSM5292179 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292179 + + + + + + + GEO Accession + GSM5292179 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952907 + SAMN19117486 + GSM5292179 + + 191114_PN_308_snRNA-E12 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 308 + + + disease state + PN + + + + + + + SRS8952907 + SAMN19117486 + GSM5292179 + + + + + + + SRR14511648 + GSM5292179_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_308_snRNA-E12_S14_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_308_snRNA-E12_S14_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_308_snRNA-E12_S14_L001_I1_001.fastq.gz + + + + + + SRS8952907 + SAMN19117486 + GSM5292179 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511649 + GSM5292179_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_308_snRNA-E12_S14_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_308_snRNA-E12_S14_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_308_snRNA-E12_S14_L002_I1_001.fastq.gz + + + + + + SRS8952907 + SAMN19117486 + GSM5292179 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857424 + + GSM5292178: 191114_PN_307_snRNA-E11; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952906 + GSM5292178 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292178 + + + + + + + GEO Accession + GSM5292178 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952906 + SAMN19117487 + GSM5292178 + + 191114_PN_307_snRNA-E11 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 307 + + + disease state + PN + + + + + + + SRS8952906 + SAMN19117487 + GSM5292178 + + + + + + + SRR14511646 + GSM5292178_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_307_snRNA-E11_S13_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_307_snRNA-E11_S13_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_307_snRNA-E11_S13_L001_I1_001.fastq.gz + + + + + + SRS8952906 + SAMN19117487 + GSM5292178 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511647 + GSM5292178_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_307_snRNA-E11_S13_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_307_snRNA-E11_S13_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_307_snRNA-E11_S13_L002_I1_001.fastq.gz + + + + + + SRS8952906 + SAMN19117487 + GSM5292178 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857423 + + GSM5292177: 191114_PN_306_snRNA-E10; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952905 + GSM5292177 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292177 + + + + + + + GEO Accession + GSM5292177 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952905 + SAMN19117488 + GSM5292177 + + 191114_PN_306_snRNA-E10 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 306 + + + disease state + PN + + + + + + + SRS8952905 + SAMN19117488 + GSM5292177 + + + + + + + SRR14511644 + GSM5292177_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_306_snRNA-E10_S16_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_306_snRNA-E10_S16_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_306_snRNA-E10_S16_L001_I1_001.fastq.gz + + + + + + SRS8952905 + SAMN19117488 + GSM5292177 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511645 + GSM5292177_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_306_snRNA-E10_S16_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_306_snRNA-E10_S16_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_306_snRNA-E10_S16_L002_I1_001.fastq.gz + + + + + + SRS8952905 + SAMN19117488 + GSM5292177 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857422 + + GSM5292176: 191114_PN_304_snRNA-E9; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952904 + GSM5292176 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292176 + + + + + + + GEO Accession + GSM5292176 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952904 + SAMN19117489 + GSM5292176 + + 191114_PN_304_snRNA-E9 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 304 + + + disease state + PN + + + + + + + SRS8952904 + SAMN19117489 + GSM5292176 + + + + + + + SRR14511642 + GSM5292176_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_304_snRNA-E9_S15_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_304_snRNA-E9_S15_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_304_snRNA-E9_S15_L001_I1_001.fastq.gz + + + + + + SRS8952904 + SAMN19117489 + GSM5292176 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511643 + GSM5292176_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_304_snRNA-E9_S15_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_304_snRNA-E9_S15_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_304_snRNA-E9_S15_L002_I1_001.fastq.gz + + + + + + SRS8952904 + SAMN19117489 + GSM5292176 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857421 + + GSM5292175: 191114_PN_303_snRNA-E8; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952903 + GSM5292175 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292175 + + + + + + + GEO Accession + GSM5292175 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952903 + SAMN19117490 + GSM5292175 + + 191114_PN_303_snRNA-E8 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 303 + + + disease state + PN + + + + + + + SRS8952903 + SAMN19117490 + GSM5292175 + + + + + + + SRR14511640 + GSM5292175_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_303_snRNA-E8_S14_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_303_snRNA-E8_S14_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_303_snRNA-E8_S14_L001_I1_001.fastq.gz + + + + + + SRS8952903 + SAMN19117490 + GSM5292175 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511641 + GSM5292175_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_303_snRNA-E8_S14_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_303_snRNA-E8_S14_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_303_snRNA-E8_S14_L002_I1_001.fastq.gz + + + + + + SRS8952903 + SAMN19117490 + GSM5292175 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857420 + + GSM5292174: 191114_PN_301_snRNA-E7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952902 + GSM5292174 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292174 + + + + + + + GEO Accession + GSM5292174 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952902 + SAMN19117491 + GSM5292174 + + 191114_PN_301_snRNA-E7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 301 + + + disease state + PN + + + + + + + SRS8952902 + SAMN19117491 + GSM5292174 + + + + + + + SRR14511638 + GSM5292174_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_301_snRNA-E7_S13_L001_R1_001.fastq.gz --read2PairFiles=191114_PN_301_snRNA-E7_S13_L001_R2_001.fastq.gz --read3PairFiles=191114_PN_301_snRNA-E7_S13_L001_I1_001.fastq.gz + + + + + + SRS8952902 + SAMN19117491 + GSM5292174 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511639 + GSM5292174_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191114_PN_301_snRNA-E7_S13_L002_R1_001.fastq.gz --read2PairFiles=191114_PN_301_snRNA-E7_S13_L002_R2_001.fastq.gz --read3PairFiles=191114_PN_301_snRNA-E7_S13_L002_I1_001.fastq.gz + + + + + + SRS8952902 + SAMN19117491 + GSM5292174 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857419 + + GSM5292173: 191113_FTLD_229_snRNA-E6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952901 + GSM5292173 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292173 + + + + + + + GEO Accession + GSM5292173 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952901 + SAMN19117492 + GSM5292173 + + 191113_FTLD_229_snRNA-E6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 229 + + + disease state + c9FTLD + + + + + + + SRS8952901 + SAMN19117492 + GSM5292173 + + + + + + + SRR14511636 + GSM5292173_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_229_snRNA-E6_S12_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_229_snRNA-E6_S12_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_229_snRNA-E6_S12_L001_I1_001.fastq.gz + + + + + + SRS8952901 + SAMN19117492 + GSM5292173 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511637 + GSM5292173_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_229_snRNA-E6_S12_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_229_snRNA-E6_S12_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_229_snRNA-E6_S12_L002_I1_001.fastq.gz + + + + + + SRS8952901 + SAMN19117492 + GSM5292173 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857418 + + GSM5292172: 191113_FTLD_228_snRNA-E5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952900 + GSM5292172 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292172 + + + + + + + GEO Accession + GSM5292172 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952900 + SAMN19117493 + GSM5292172 + + 191113_FTLD_228_snRNA-E5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 228 + + + disease state + sFTLD + + + + + + + SRS8952900 + SAMN19117493 + GSM5292172 + + + + + + + SRR14511634 + GSM5292172_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_228_snRNA-E5_S11_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_228_snRNA-E5_S11_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_228_snRNA-E5_S11_L001_I1_001.fastq.gz + + + + + + SRS8952900 + SAMN19117493 + GSM5292172 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511635 + GSM5292172_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_228_snRNA-E5_S11_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_228_snRNA-E5_S11_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_228_snRNA-E5_S11_L002_I1_001.fastq.gz + + + + + + SRS8952900 + SAMN19117493 + GSM5292172 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857417 + + GSM5292171: 191113_FTLD_226_snRNA-E4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952899 + GSM5292171 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292171 + + + + + + + GEO Accession + GSM5292171 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952899 + SAMN19117494 + GSM5292171 + + 191113_FTLD_226_snRNA-E4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 226 + + + disease state + sFTLD + + + + + + + SRS8952899 + SAMN19117494 + GSM5292171 + + + + + + + SRR14511632 + GSM5292171_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_226_snRNA-E4_S10_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_226_snRNA-E4_S10_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_226_snRNA-E4_S10_L001_I1_001.fastq.gz + + + + + + SRS8952899 + SAMN19117494 + GSM5292171 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511633 + GSM5292171_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_226_snRNA-E4_S10_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_226_snRNA-E4_S10_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_226_snRNA-E4_S10_L002_I1_001.fastq.gz + + + + + + SRS8952899 + SAMN19117494 + GSM5292171 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857416 + + GSM5292170: 191113_FTLD_225_snRNA-H5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952898 + GSM5292170 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292170 + + + + + + + GEO Accession + GSM5292170 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952898 + SAMN19117495 + GSM5292170 + + 191113_FTLD_225_snRNA-H5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 225 + + + disease state + sFTLD + + + + + + + SRS8952898 + SAMN19117495 + GSM5292170 + + + + + + + SRR14511630 + GSM5292170_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_225_snRNA-H5_S9_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_225_snRNA-H5_S9_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_225_snRNA-H5_S9_L001_I1_001.fastq.gz + + + + + + SRS8952898 + SAMN19117495 + GSM5292170 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511631 + GSM5292170_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_225_snRNA-H5_S9_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_225_snRNA-H5_S9_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_225_snRNA-H5_S9_L002_I1_001.fastq.gz + + + + + + SRS8952898 + SAMN19117495 + GSM5292170 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857415 + + GSM5292169: 191113_FTLD_224_snRNA-E2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952897 + GSM5292169 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292169 + + + + + + + GEO Accession + GSM5292169 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952897 + SAMN19117459 + GSM5292169 + + 191113_FTLD_224_snRNA-E2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 224 + + + disease state + c9FTLD + + + + + + + SRS8952897 + SAMN19117459 + GSM5292169 + + + + + + + SRR14511628 + GSM5292169_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_224_snRNA-E2_S12_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_224_snRNA-E2_S12_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_224_snRNA-E2_S12_L001_I1_001.fastq.gz + + + + + + SRS8952897 + SAMN19117459 + GSM5292169 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511629 + GSM5292169_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_224_snRNA-E2_S12_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_224_snRNA-E2_S12_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_224_snRNA-E2_S12_L002_I1_001.fastq.gz + + + + + + SRS8952897 + SAMN19117459 + GSM5292169 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857414 + + GSM5292168: 191113_FTLD_222_snRNA-E1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952896 + GSM5292168 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292168 + + + + + + + GEO Accession + GSM5292168 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952896 + SAMN19117461 + GSM5292168 + + 191113_FTLD_222_snRNA-E1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 222 + + + disease state + sFTLD + + + + + + + SRS8952896 + SAMN19117461 + GSM5292168 + + + + + + + SRR14511626 + GSM5292168_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_222_snRNA-E1_S11_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_222_snRNA-E1_S11_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_222_snRNA-E1_S11_L001_I1_001.fastq.gz + + + + + + SRS8952896 + SAMN19117461 + GSM5292168 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511627 + GSM5292168_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_222_snRNA-E1_S11_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_222_snRNA-E1_S11_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_222_snRNA-E1_S11_L002_I1_001.fastq.gz + + + + + + SRS8952896 + SAMN19117461 + GSM5292168 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857413 + + GSM5292167: 191113_FTLD_218_snRNA-H4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952895 + GSM5292167 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292167 + + + + + + + GEO Accession + GSM5292167 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952895 + SAMN19117462 + GSM5292167 + + 191113_FTLD_218_snRNA-H4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 218 + + + disease state + sFTLD + + + + + + + SRS8952895 + SAMN19117462 + GSM5292167 + + + + + + + SRR14511624 + GSM5292167_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_218_snRNA-H4_S10_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_218_snRNA-H4_S10_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_218_snRNA-H4_S10_L001_I1_001.fastq.gz + + + + + + SRS8952895 + SAMN19117462 + GSM5292167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511625 + GSM5292167_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_218_snRNA-H4_S10_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_218_snRNA-H4_S10_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_218_snRNA-H4_S10_L002_I1_001.fastq.gz + + + + + + SRS8952895 + SAMN19117462 + GSM5292167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857412 + + GSM5292166: 191113_FTLD_217_snRNA-D11; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952893 + GSM5292166 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292166 + + + + + + + GEO Accession + GSM5292166 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952893 + SAMN19117434 + GSM5292166 + + 191113_FTLD_217_snRNA-D11 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 217 + + + disease state + sFTLD + + + + + + + SRS8952893 + SAMN19117434 + GSM5292166 + + + + + + + SRR14511622 + GSM5292166_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_217_snRNA-D11_S9_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_217_snRNA-D11_S9_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_217_snRNA-D11_S9_L001_I1_001.fastq.gz + + + + + + SRS8952893 + SAMN19117434 + GSM5292166 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511623 + GSM5292166_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_217_snRNA-D11_S9_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_217_snRNA-D11_S9_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_217_snRNA-D11_S9_L002_I1_001.fastq.gz + + + + + + SRS8952893 + SAMN19117434 + GSM5292166 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857411 + + GSM5292165: 191113_FTLD_216_snRNA-H3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952894 + GSM5292165 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292165 + + + + + + + GEO Accession + GSM5292165 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952894 + SAMN19117435 + GSM5292165 + + 191113_FTLD_216_snRNA-H3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 216 + + + disease state + sFTLD + + + + + + + SRS8952894 + SAMN19117435 + GSM5292165 + + + + + + + SRR14511620 + GSM5292165_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_216_snRNA-H3_S12_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_216_snRNA-H3_S12_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_216_snRNA-H3_S12_L001_I1_001.fastq.gz + + + + + + SRS8952894 + SAMN19117435 + GSM5292165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511621 + GSM5292165_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_216_snRNA-H3_S12_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_216_snRNA-H3_S12_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_216_snRNA-H3_S12_L002_I1_001.fastq.gz + + + + + + SRS8952894 + SAMN19117435 + GSM5292165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857410 + + GSM5292164: 191113_FTLD_214_snRNA-D9; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952892 + GSM5292164 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292164 + + + + + + + GEO Accession + GSM5292164 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952892 + SAMN19117436 + GSM5292164 + + 191113_FTLD_214_snRNA-D9 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 214 + + + disease state + c9FTLD + + + + + + + SRS8952892 + SAMN19117436 + GSM5292164 + + + + + + + SRR14511618 + GSM5292164_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_214_snRNA-D9_S11_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_214_snRNA-D9_S11_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_214_snRNA-D9_S11_L001_I1_001.fastq.gz + + + + + + SRS8952892 + SAMN19117436 + GSM5292164 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511619 + GSM5292164_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_214_snRNA-D9_S11_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_214_snRNA-D9_S11_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_214_snRNA-D9_S11_L002_I1_001.fastq.gz + + + + + + SRS8952892 + SAMN19117436 + GSM5292164 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857409 + + GSM5292163: 191113_FTLD_211_snRNA-D7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952891 + GSM5292163 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292163 + + + + + + + GEO Accession + GSM5292163 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952891 + SAMN19117437 + GSM5292163 + + 191113_FTLD_211_snRNA-D7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 211 + + + disease state + sFTLD + + + + + + + SRS8952891 + SAMN19117437 + GSM5292163 + + + + + + + SRR14511616 + GSM5292163_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_211_snRNA-D7_S9_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_211_snRNA-D7_S9_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_211_snRNA-D7_S9_L001_I1_001.fastq.gz + + + + + + SRS8952891 + SAMN19117437 + GSM5292163 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511617 + GSM5292163_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_211_snRNA-D7_S9_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_211_snRNA-D7_S9_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_211_snRNA-D7_S9_L002_I1_001.fastq.gz + + + + + + SRS8952891 + SAMN19117437 + GSM5292163 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857408 + + GSM5292162: 191113_FTLD_209_snRNA-D6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952890 + GSM5292162 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292162 + + + + + + + GEO Accession + GSM5292162 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952890 + SAMN19117438 + GSM5292162 + + 191113_FTLD_209_snRNA-D6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 209 + + + disease state + sFTLD + + + + + + + SRS8952890 + SAMN19117438 + GSM5292162 + + + + + + + SRR14511614 + GSM5292162_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_209_snRNA-D6_S12_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_209_snRNA-D6_S12_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_209_snRNA-D6_S12_L001_I1_001.fastq.gz + + + + + + SRS8952890 + SAMN19117438 + GSM5292162 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511615 + GSM5292162_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_209_snRNA-D6_S12_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_209_snRNA-D6_S12_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_209_snRNA-D6_S12_L002_I1_001.fastq.gz + + + + + + SRS8952890 + SAMN19117438 + GSM5292162 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857407 + + GSM5292161: 191113_FTLD_207_snRNA-D5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952889 + GSM5292161 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292161 + + + + + + + GEO Accession + GSM5292161 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952889 + SAMN19117439 + GSM5292161 + + 191113_FTLD_207_snRNA-D5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 207 + + + disease state + sFTLD + + + + + + + SRS8952889 + SAMN19117439 + GSM5292161 + + + + + + + SRR14511612 + GSM5292161_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_207_snRNA-D5_S11_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_207_snRNA-D5_S11_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_207_snRNA-D5_S11_L001_I1_001.fastq.gz + + + + + + SRS8952889 + SAMN19117439 + GSM5292161 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511613 + GSM5292161_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_207_snRNA-D5_S11_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_207_snRNA-D5_S11_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_207_snRNA-D5_S11_L002_I1_001.fastq.gz + + + + + + SRS8952889 + SAMN19117439 + GSM5292161 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857406 + + GSM5292160: 191113_FTLD_204_snRNA-D4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952888 + GSM5292160 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292160 + + + + + + + GEO Accession + GSM5292160 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952888 + SAMN19117440 + GSM5292160 + + 191113_FTLD_204_snRNA-D4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 204 + + + disease state + sFTLD + + + + + + + SRS8952888 + SAMN19117440 + GSM5292160 + + + + + + + SRR14511610 + GSM5292160_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_204_snRNA-D4_S10_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_204_snRNA-D4_S10_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_204_snRNA-D4_S10_L001_I1_001.fastq.gz + + + + + + SRS8952888 + SAMN19117440 + GSM5292160 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511611 + GSM5292160_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_204_snRNA-D4_S10_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_204_snRNA-D4_S10_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_204_snRNA-D4_S10_L002_I1_001.fastq.gz + + + + + + SRS8952888 + SAMN19117440 + GSM5292160 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857405 + + GSM5292159: 191113_FTLD_202_snRNA-D3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952887 + GSM5292159 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292159 + + + + + + + GEO Accession + GSM5292159 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952887 + SAMN19117441 + GSM5292159 + + 191113_FTLD_202_snRNA-D3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 202 + + + disease state + sFTLD + + + + + + + SRS8952887 + SAMN19117441 + GSM5292159 + + + + + + + SRR14511608 + GSM5292159_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_202_snRNA-D3_S9_L001_R1_001.fastq.gz --read2PairFiles=191113_FTLD_202_snRNA-D3_S9_L001_R2_001.fastq.gz --read3PairFiles=191113_FTLD_202_snRNA-D3_S9_L001_I1_001.fastq.gz + + + + + + SRS8952887 + SAMN19117441 + GSM5292159 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511609 + GSM5292159_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191113_FTLD_202_snRNA-D3_S9_L002_R1_001.fastq.gz --read2PairFiles=191113_FTLD_202_snRNA-D3_S9_L002_R2_001.fastq.gz --read3PairFiles=191113_FTLD_202_snRNA-D3_S9_L002_I1_001.fastq.gz + + + + + + SRS8952887 + SAMN19117441 + GSM5292159 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857404 + + GSM5292158: 191112_ALS_130_snRNA-A5; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952886 + GSM5292158 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292158 + + + + + + + GEO Accession + GSM5292158 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952886 + SAMN19117442 + GSM5292158 + + 191112_ALS_130_snRNA-A5 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 130 + + + disease state + c9ALS + + + + + + + SRS8952886 + SAMN19117442 + GSM5292158 + + + + + + + SRR14511606 + GSM5292158_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_130_snRNA-A5_S8_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_130_snRNA-A5_S8_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_130_snRNA-A5_S8_L001_I1_001.fastq.gz + + + + + + SRS8952886 + SAMN19117442 + GSM5292158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511607 + GSM5292158_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_130_snRNA-A5_S8_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_130_snRNA-A5_S8_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_130_snRNA-A5_S8_L002_I1_001.fastq.gz + + + + + + SRS8952886 + SAMN19117442 + GSM5292158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857403 + + GSM5292157: 191112_ALS_129_snRNA-A2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952885 + GSM5292157 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292157 + + + + + + + GEO Accession + GSM5292157 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952885 + SAMN19117443 + GSM5292157 + + 191112_ALS_129_snRNA-A2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 129 + + + disease state + c9ALS + + + + + + + SRS8952885 + SAMN19117443 + GSM5292157 + + + + + + + SRR14511604 + GSM5292157_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_129_snRNA-A2_S7_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_129_snRNA-A2_S7_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_129_snRNA-A2_S7_L001_I1_001.fastq.gz + + + + + + SRS8952885 + SAMN19117443 + GSM5292157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511605 + GSM5292157_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_129_snRNA-A2_S7_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_129_snRNA-A2_S7_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_129_snRNA-A2_S7_L002_I1_001.fastq.gz + + + + + + SRS8952885 + SAMN19117443 + GSM5292157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857402 + + GSM5292156: 191112_ALS_128_snRNA-A7; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952884 + GSM5292156 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292156 + + + + + + + GEO Accession + GSM5292156 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952884 + SAMN19117444 + GSM5292156 + + 191112_ALS_128_snRNA-A7 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 128 + + + disease state + c9ALS + + + + + + + SRS8952884 + SAMN19117444 + GSM5292156 + + + + + + + SRR14511602 + GSM5292156_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_128_snRNA-A7_S6_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_128_snRNA-A7_S6_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_128_snRNA-A7_S6_L001_I1_001.fastq.gz + + + + + + SRS8952884 + SAMN19117444 + GSM5292156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511603 + GSM5292156_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_128_snRNA-A7_S6_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_128_snRNA-A7_S6_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_128_snRNA-A7_S6_L002_I1_001.fastq.gz + + + + + + SRS8952884 + SAMN19117444 + GSM5292156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857401 + + GSM5292155: 191112_ALS_127_snRNA-A4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952883 + GSM5292155 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292155 + + + + + + + GEO Accession + GSM5292155 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952883 + SAMN19117445 + GSM5292155 + + 191112_ALS_127_snRNA-A4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 127 + + + disease state + sALS + + + + + + + SRS8952883 + SAMN19117445 + GSM5292155 + + + + + + + SRR14511600 + GSM5292155_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_127_snRNA-A4_S5_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_127_snRNA-A4_S5_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_127_snRNA-A4_S5_L001_I1_001.fastq.gz + + + + + + SRS8952883 + SAMN19117445 + GSM5292155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511601 + GSM5292155_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_127_snRNA-A4_S5_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_127_snRNA-A4_S5_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_127_snRNA-A4_S5_L002_I1_001.fastq.gz + + + + + + SRS8952883 + SAMN19117445 + GSM5292155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857400 + + GSM5292154: 191112_ALS_126_snRNA-A6; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952882 + GSM5292154 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292154 + + + + + + + GEO Accession + GSM5292154 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952882 + SAMN19117446 + GSM5292154 + + 191112_ALS_126_snRNA-A6 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 126 + + + disease state + sALS + + + + + + + SRS8952882 + SAMN19117446 + GSM5292154 + + + + + + + SRR14511598 + GSM5292154_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_126_snRNA-A6_S8_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_126_snRNA-A6_S8_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_126_snRNA-A6_S8_L001_I1_001.fastq.gz + + + + + + SRS8952882 + SAMN19117446 + GSM5292154 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511599 + GSM5292154_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_126_snRNA-A6_S8_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_126_snRNA-A6_S8_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_126_snRNA-A6_S8_L002_I1_001.fastq.gz + + + + + + SRS8952882 + SAMN19117446 + GSM5292154 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857399 + + GSM5292153: 191112_ALS_124_snRNA-A3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952880 + GSM5292153 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292153 + + + + + + + GEO Accession + GSM5292153 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952880 + SAMN19117447 + GSM5292153 + + 191112_ALS_124_snRNA-A3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 124 + + + disease state + sALS + + + + + + + SRS8952880 + SAMN19117447 + GSM5292153 + + + + + + + SRR14511596 + GSM5292153_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_124_snRNA-A3_S7_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_124_snRNA-A3_S7_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_124_snRNA-A3_S7_L001_I1_001.fastq.gz + + + + + + SRS8952880 + SAMN19117447 + GSM5292153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511597 + GSM5292153_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_124_snRNA-A3_S7_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_124_snRNA-A3_S7_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_124_snRNA-A3_S7_L002_I1_001.fastq.gz + + + + + + SRS8952880 + SAMN19117447 + GSM5292153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857398 + + GSM5292152: 191112_ALS_122_snRNA-D2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952879 + GSM5292152 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292152 + + + + + + + GEO Accession + GSM5292152 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952879 + SAMN19117448 + GSM5292152 + + 191112_ALS_122_snRNA-D2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 122 + + + disease state + sALS + + + + + + + SRS8952879 + SAMN19117448 + GSM5292152 + + + + + + + SRR14511594 + GSM5292152_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_122_snRNA-D2_S6_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_122_snRNA-D2_S6_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_122_snRNA-D2_S6_L001_I1_001.fastq.gz + + + + + + SRS8952879 + SAMN19117448 + GSM5292152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511595 + GSM5292152_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_122_snRNA-D2_S6_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_122_snRNA-D2_S6_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_122_snRNA-D2_S6_L002_I1_001.fastq.gz + + + + + + SRS8952879 + SAMN19117448 + GSM5292152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857397 + + GSM5292151: 191112_ALS_120_snRNA-A1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952881 + GSM5292151 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292151 + + + + + + + GEO Accession + GSM5292151 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952881 + SAMN19117449 + GSM5292151 + + 191112_ALS_120_snRNA-A1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 120 + + + disease state + sALS + + + + + + + SRS8952881 + SAMN19117449 + GSM5292151 + + + + + + + SRR14511592 + GSM5292151_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_120_snRNA-A1_S5_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_120_snRNA-A1_S5_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_120_snRNA-A1_S5_L001_I1_001.fastq.gz + + + + + + SRS8952881 + SAMN19117449 + GSM5292151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511593 + GSM5292151_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_120_snRNA-A1_S5_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_120_snRNA-A1_S5_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_120_snRNA-A1_S5_L002_I1_001.fastq.gz + + + + + + SRS8952881 + SAMN19117449 + GSM5292151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857396 + + GSM5292150: 191112_ALS_118_snRNA-C4; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952878 + GSM5292150 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292150 + + + + + + + GEO Accession + GSM5292150 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952878 + SAMN19117450 + GSM5292150 + + 191112_ALS_118_snRNA-C4 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 118 + + + disease state + sALS + + + + + + + SRS8952878 + SAMN19117450 + GSM5292150 + + + + + + + SRR14511590 + GSM5292150_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_118_snRNA-C4_S8_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_118_snRNA-C4_S8_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_118_snRNA-C4_S8_L001_I1_001.fastq.gz + + + + + + SRS8952878 + SAMN19117450 + GSM5292150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511591 + GSM5292150_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_118_snRNA-C4_S8_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_118_snRNA-C4_S8_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_118_snRNA-C4_S8_L002_I1_001.fastq.gz + + + + + + SRS8952878 + SAMN19117450 + GSM5292150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857395 + + GSM5292149: 191112_ALS_117_snRNA-C3; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952877 + GSM5292149 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292149 + + + + + + + GEO Accession + GSM5292149 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952877 + SAMN19117451 + GSM5292149 + + 191112_ALS_117_snRNA-C3 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 117 + + + disease state + sALS + + + + + + + SRS8952877 + SAMN19117451 + GSM5292149 + + + + + + + SRR14511588 + GSM5292149_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_117_snRNA-C3_S7_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_117_snRNA-C3_S7_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_117_snRNA-C3_S7_L001_I1_001.fastq.gz + + + + + + SRS8952877 + SAMN19117451 + GSM5292149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511589 + GSM5292149_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_117_snRNA-C3_S7_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_117_snRNA-C3_S7_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_117_snRNA-C3_S7_L002_I1_001.fastq.gz + + + + + + SRS8952877 + SAMN19117451 + GSM5292149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857394 + + GSM5292148: 191112_ALS_116_snRNA-C2; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952876 + GSM5292148 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292148 + + + + + + + GEO Accession + GSM5292148 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952876 + SAMN19117452 + GSM5292148 + + 191112_ALS_116_snRNA-C2 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 116 + + + disease state + sALS + + + + + + + SRS8952876 + SAMN19117452 + GSM5292148 + + + + + + + SRR14511586 + GSM5292148_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_116_snRNA-C2_S6_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_116_snRNA-C2_S6_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_116_snRNA-C2_S6_L001_I1_001.fastq.gz + + + + + + SRS8952876 + SAMN19117452 + GSM5292148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511587 + GSM5292148_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_116_snRNA-C2_S6_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_116_snRNA-C2_S6_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_116_snRNA-C2_S6_L002_I1_001.fastq.gz + + + + + + SRS8952876 + SAMN19117452 + GSM5292148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857393 + + GSM5292147: 191112_ALS_115_snRNA-C1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952875 + GSM5292147 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292147 + + + + + + + GEO Accession + GSM5292147 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952875 + SAMN19117453 + GSM5292147 + + 191112_ALS_115_snRNA-C1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 115 + + + disease state + c9ALS + + + + + + + SRS8952875 + SAMN19117453 + GSM5292147 + + + + + + + SRR14511584 + GSM5292147_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_115_snRNA-C1_S5_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_115_snRNA-C1_S5_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_115_snRNA-C1_S5_L001_I1_001.fastq.gz + + + + + + SRS8952875 + SAMN19117453 + GSM5292147 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511585 + GSM5292147_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_115_snRNA-C1_S5_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_115_snRNA-C1_S5_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_115_snRNA-C1_S5_L002_I1_001.fastq.gz + + + + + + SRS8952875 + SAMN19117453 + GSM5292147 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857392 + + GSM5292146: 191112_ALS_114_snRNA-B12; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952874 + GSM5292146 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292146 + + + + + + + GEO Accession + GSM5292146 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952874 + SAMN19117454 + GSM5292146 + + 191112_ALS_114_snRNA-B12 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 114 + + + disease state + c9ALS + + + + + + + SRS8952874 + SAMN19117454 + GSM5292146 + + + + + + + SRR14511582 + GSM5292146_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_114_snRNA-B12_S8_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_114_snRNA-B12_S8_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_114_snRNA-B12_S8_L001_I1_001.fastq.gz + + + + + + SRS8952874 + SAMN19117454 + GSM5292146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511583 + GSM5292146_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_114_snRNA-B12_S8_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_114_snRNA-B12_S8_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_114_snRNA-B12_S8_L002_I1_001.fastq.gz + + + + + + SRS8952874 + SAMN19117454 + GSM5292146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857391 + + GSM5292145: 191112_ALS_112_snRNA-D1; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952873 + GSM5292145 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292145 + + + + + + + GEO Accession + GSM5292145 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952873 + SAMN19117455 + GSM5292145 + + 191112_ALS_112_snRNA-D1 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 112 + + + disease state + sALS + + + + + + + SRS8952873 + SAMN19117455 + GSM5292145 + + + + + + + SRR14511580 + GSM5292145_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_112_snRNA-D1_S7_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_112_snRNA-D1_S7_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_112_snRNA-D1_S7_L001_I1_001.fastq.gz + + + + + + SRS8952873 + SAMN19117455 + GSM5292145 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511581 + GSM5292145_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_112_snRNA-D1_S7_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_112_snRNA-D1_S7_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_112_snRNA-D1_S7_L002_I1_001.fastq.gz + + + + + + SRS8952873 + SAMN19117455 + GSM5292145 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857390 + + GSM5292144: 191112_ALS_111_snRNA-B10; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952872 + GSM5292144 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292144 + + + + + + + GEO Accession + GSM5292144 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952872 + SAMN19117457 + GSM5292144 + + 191112_ALS_111_snRNA-B10 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 111 + + + disease state + sALS + + + + + + + SRS8952872 + SAMN19117457 + GSM5292144 + + + + + + + SRR14511578 + GSM5292144_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_111_snRNA-B10_S6_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_111_snRNA-B10_S6_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_111_snRNA-B10_S6_L001_I1_001.fastq.gz + + + + + + SRS8952872 + SAMN19117457 + GSM5292144 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511579 + GSM5292144_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_111_snRNA-B10_S6_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_111_snRNA-B10_S6_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_111_snRNA-B10_S6_L002_I1_001.fastq.gz + + + + + + SRS8952872 + SAMN19117457 + GSM5292144 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX10857389 + + GSM5292143: 191112_ALS_110_snRNA-B9; Homo sapiens; RNA-Seq + + + SRP319497 + + + + + + + SRS8952871 + GSM5292143 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA. Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual. Molecules barcoded with 10x Gene Expression 3' kit v3. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305292143 + + + + + + + GEO Accession + GSM5292143 + + + + + + SRA1231427 + GEO: GSE174332 + + + + NCBI + + + Geo + Curators + + + + + + SRP319497 + PRJNA729486 + GSE174332 + + + Single-cell dissection of the primary motor cortex in ALS and FTLD patients. + + Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable and fatal neurodegenerative conditions. While distinct, they share many clinical, genetic, and pathological characteristics, and both show highly vulnerable layer 5 extratelencephalic-projecting cortical populations, including Betz cells in ALS2 and von Economo neurons (VENs) in FTLD. Here, we report the first single-cell atlas of the human primary motor cortex and its changes in ALS and FTLD across ~380,000 nuclei from 64 control, sporadic and C9orf72-associated ALS and FTLD individuals. We identify 46 transcriptionally distinct cellular subtypes including two Betz-cell subtypes, and observe a previously-unappreciated molecular similarity between Betz cells and VENs of the frontal insula. Most dysregulated genes and pathways were shared, including stress response, ribosome function, oxidative phosphorylation, synaptic vesicle cycle, endoplasmic reticulum protein processing, and autophagy. Betz cells and SCN4B+ long-range projecting L3/L5 cells are the most transcriptionally affected in both ALS and FTLD. Lastly, the VEN/Betz-cell-enriched dysregulated gene POU3F1 co-localizes with TDP-43 aggregates in Betz cells. Overall design: Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration **This dataset has been replaced by BioProject PRJNA1073234** + GSE174332 + + + + + SRS8952871 + SAMN19117458 + GSM5292143 + + 191112_ALS_110_snRNA-B9 + + 9606 + Homo sapiens + + + + + bioproject + 729486 + + + + + + + source_name + Motor Cortex + + + tissue + Motor Cortex + + + ID + 110 + + + disease state + sALS + + + + + + + SRS8952871 + SAMN19117458 + GSM5292143 + + + + + + + SRR14511576 + GSM5292143_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_110_snRNA-B9_S5_L001_R1_001.fastq.gz --read2PairFiles=191112_ALS_110_snRNA-B9_S5_L001_R2_001.fastq.gz --read3PairFiles=191112_ALS_110_snRNA-B9_S5_L001_I1_001.fastq.gz + + + + + + SRS8952871 + SAMN19117458 + GSM5292143 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14511577 + GSM5292143_r2 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=191112_ALS_110_snRNA-B9_S5_L002_R1_001.fastq.gz --read2PairFiles=191112_ALS_110_snRNA-B9_S5_L002_R2_001.fastq.gz --read3PairFiles=191112_ALS_110_snRNA-B9_S5_L002_I1_001.fastq.gz + + + + + + SRS8952871 + SAMN19117458 + GSM5292143 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE174667.xml b/tests/data/GSE174667.xml new file mode 100644 index 0000000..598f1ff --- /dev/null +++ b/tests/data/GSE174667.xml @@ -0,0 +1,3706 @@ + + + + + + + SRX10930041 + + GSM5322187: chikv-3; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013417 + GSM5322187 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322187 + + + + + + + GEO Accession + GSM5322187 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013417 + SAMN19245907 + GSM5322187 + + chikv-3 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + chikv + + + time + 24 hpi + + + + + + + SRS9013417 + SAMN19245907 + GSM5322187 + + + + + + + SRR14582702 + GSM5322187_r1 + + + + + + SRS9013417 + SAMN19245907 + GSM5322187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX10930040 + + GSM5322186: chikv-2; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013416 + GSM5322186 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322186 + + + + + + + GEO Accession + GSM5322186 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013416 + SAMN19245909 + GSM5322186 + + chikv-2 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + chikv + + + time + 24 hpi + + + + + + + SRS9013416 + SAMN19245909 + GSM5322186 + + + + + + + SRR14582694 + GSM5322186_r1 + + + + + + SRS9013416 + SAMN19245909 + GSM5322186 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX10930039 + + GSM5322185: chikv-1; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013415 + GSM5322185 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322185 + + + + + + + GEO Accession + GSM5322185 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013415 + SAMN19245910 + GSM5322185 + + chikv-1 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + chikv + + + time + 24 hpi + + + + + + + SRS9013415 + SAMN19245910 + GSM5322185 + + + + + + + SRR14582686 + GSM5322185_r1 + + + + + + SRS9013415 + SAMN19245910 + GSM5322185 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX10930038 + + GSM5322184: mock-3; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013414 + GSM5322184 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322184 + + + + + + + GEO Accession + GSM5322184 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013414 + SAMN19245912 + GSM5322184 + + mock-3 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + mock + + + time + 24 hpi + + + + + + + SRS9013414 + SAMN19245912 + GSM5322184 + + + + + + + SRR14582678 + GSM5322184_r1 + + + + + + SRS9013414 + SAMN19245912 + GSM5322184 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX10930037 + + GSM5322183: mock-2; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013413 + GSM5322183 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322183 + + + + + + + GEO Accession + GSM5322183 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013413 + SAMN19245914 + GSM5322183 + + mock-2 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + mock + + + time + 24 hpi + + + + + + + SRS9013413 + SAMN19245914 + GSM5322183 + + + + + + + SRR14582670 + GSM5322183_r1 + + + + + + SRS9013413 + SAMN19245914 + GSM5322183 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX10930036 + + GSM5322182: mock-1; Mus musculus; RNA-Seq + + + SRP320410 + + + + + + + SRS9013412 + GSM5322182 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click's medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer's instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry. Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305322182 + + + + + + + GEO Accession + GSM5322182 + + + + + + SRA1233983 + GEO: GSE174667 + + + + NCBI + + + Geo + Curators + + + + + + SRP320410 + PRJNA730926 + GSE174667 + + + MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination + + While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections. Overall design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing. + GSE174667 + + + + + pubmed + 34618370 + + + + + + + SRS9013412 + SAMN19245915 + GSM5322182 + + mock-1 + + 10090 + Mus musculus + + + + + bioproject + 730926 + + + + + + + source_name + Lymph node + + + tissue + Lymph node + + + strain + C57BL/6 + + + genotype + WT + + + inoculation + mock + + + time + 24 hpi + + + + + + + SRS9013412 + SAMN19245915 + GSM5322182 + + + + + + + SRR14582662 + GSM5322182_r1 + + + + + + SRS9013412 + SAMN19245915 + GSM5322182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR14582664 + GSM5322182_r3 + + + + + + SRS9013412 + SAMN19245915 + GSM5322182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR14582666 + GSM5322182_r5 + + + + + + SRS9013412 + SAMN19245915 + GSM5322182 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + diff --git a/tests/data/GSE178257.xml b/tests/data/GSE178257.xml new file mode 100644 index 0000000..da3d262 --- /dev/null +++ b/tests/data/GSE178257.xml @@ -0,0 +1,2029 @@ + + + + + + + SRX11150190 + + GSM5385965: VCPFF-CAMK2_1M-9: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211920 + GSM5385965 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385965 + + + + + + + GEO Accession + GSM5385965 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211920 + SAMN19714116 + GSM5385965 + + VCPFF-CAMK2_1M-9: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 1 month + + + + + + + SRS9211920 + SAMN19714116 + GSM5385965 + + + + + + + SRR14820255 + GSM5385965_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211920 + SAMN19714116 + GSM5385965 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150189 + + GSM5385964: VCPFF-CAMK2_1M-8: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211919 + GSM5385964 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385964 + + + + + + + GEO Accession + GSM5385964 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211919 + SAMN19714117 + GSM5385964 + + VCPFF-CAMK2_1M-8: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 1 month + + + + + + + SRS9211919 + SAMN19714117 + GSM5385964 + + + + + + + SRR14820254 + GSM5385964_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211919 + SAMN19714117 + GSM5385964 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150188 + + GSM5385963: VCPFF-CAMK2_1M-7: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211918 + GSM5385963 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385963 + + + + + + + GEO Accession + GSM5385963 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211918 + SAMN19714091 + GSM5385963 + + VCPFF-CAMK2_1M-7: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 1 month + + + + + + + SRS9211918 + SAMN19714091 + GSM5385963 + + + + + + + SRR14820253 + GSM5385963_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211918 + SAMN19714091 + GSM5385963 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150187 + + GSM5385962: VCPFF-CAMK2_2M-6: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211917 + GSM5385962 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385962 + + + + + + + GEO Accession + GSM5385962 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211917 + SAMN19714092 + GSM5385962 + + VCPFF-CAMK2_2M-6: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211917 + SAMN19714092 + GSM5385962 + + + + + + + SRR14820252 + GSM5385962_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211917 + SAMN19714092 + GSM5385962 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + +
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+ + + + + + + + + + + + + + + + SRX11150186 + + GSM5385961: VCPFF-CAMK2_2M-5: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211916 + GSM5385961 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385961 + + + + + + + GEO Accession + GSM5385961 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211916 + SAMN19714093 + GSM5385961 + + VCPFF-CAMK2_2M-5: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211916 + SAMN19714093 + GSM5385961 + + + + + + + SRR14820251 + GSM5385961_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211916 + SAMN19714093 + GSM5385961 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150185 + + GSM5385960: VCPFF-CAMK2_2M-4: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211915 + GSM5385960 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385960 + + + + + + + GEO Accession + GSM5385960 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211915 + SAMN19714094 + GSM5385960 + + VCPFF-CAMK2_2M-4: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice + + + mouse genotype + VCPfl/fl;Camk2-Cre + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211915 + SAMN19714094 + GSM5385960 + + + + + + + SRR14820250 + GSM5385960_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211915 + SAMN19714094 + GSM5385960 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150184 + + GSM5385959: VCPFF-3: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211913 + GSM5385959 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385959 + + + + + + + GEO Accession + GSM5385959 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211913 + SAMN19714097 + GSM5385959 + + VCPFF-3: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + + mouse genotype + VCPfl/fl + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211913 + SAMN19714097 + GSM5385959 + + + + + + + SRR14820249 + GSM5385959_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211913 + SAMN19714097 + GSM5385959 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150183 + + GSM5385958: VCPFF-2: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211912 + GSM5385958 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385958 + + + + + + + GEO Accession + GSM5385958 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211912 + SAMN19714095 + GSM5385958 + + VCPFF-2: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + + mouse genotype + VCPfl/fl + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211912 + SAMN19714095 + GSM5385958 + + + + + + + SRR14820248 + GSM5385958_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211912 + SAMN19714095 + GSM5385958 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11150182 + + GSM5385957: VCPFF-1: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice; Mus musculus; RNA-Seq + + + SRP324150 + + + + + + + SRS9211914 + GSM5385957 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer. Isolated single nuclei were subjected to droplet-based 3' end massively parallel single-cell RNA sequencing using Chromium Single Cell 5' Reagent Kits as per manufacturer's instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305385957 + + + + + + + GEO Accession + GSM5385957 + + + + + + SRA1245390 + GEO: GSE178257 + + + + NCBI + + + Geo + Curators + + + + + + SRP324150 + PRJNA738150 + GSE178257 + + + Neuronal VCP loss of function recapitulates FTLD-TDP pathology + + The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency. Overall design: Droplet-based 3' end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers. + GSE178257 + + + + + pubmed + 34289347 + + + + + + + SRS9211914 + SAMN19714096 + GSM5385957 + + VCPFF-1: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + 10090 + Mus musculus + + + + + bioproject + 738150 + + + + + + + source_name + Isolated single nuclei from cortex of 2 month old VCPfl/fl mice + + + mouse genotype + VCPfl/fl + + + strain + B6 + + + tissue + nuclei of brain + + + age + 2 months + + + + + + + SRS9211914 + SAMN19714096 + GSM5385957 + + + + + + + SRR14820247 + GSM5385957_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9211914 + SAMN19714096 + GSM5385957 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE179135.xml b/tests/data/GSE179135.xml new file mode 100644 index 0000000..9a2173a --- /dev/null +++ b/tests/data/GSE179135.xml @@ -0,0 +1,3761 @@ + + + + + + + SRX11287786 + + GSM5410492: M3; Homo sapiens; RNA-Seq + + + SRP326057 + + + + + + + SRS9316013 + GSM5410492 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After the perichondrium was stripped on ice immediately, all auricular cartilage samples were minced into ~1 mm2 pieces and digested for 10 minutes with trypsin at 37°C to remove residual tissue attached to cartilage tissue. The cell suspension was loaded onto the Chromium single-cell controller (10x Genomics, USA) to generate single-cell gel beads in the emulsion (GEMs) by using Single Cell 3′ Library and Gel Bead Kit V3 (10x Genomics, USA) and Chromium Single Cell A Chip Kit (10x Genomics, USA) (performed by CapitalBio Technology, Beijing) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305410492 + + + + + + + GEO Accession + GSM5410492 + + + + + + SRA1252149 + GEO: GSE179135 + + + + NCBI + + + Geo + Curators + + + + + + SRP326057 + PRJNA742395 + GSE179135 + + + Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population + + As one of most common birth defects worldwide, microtia results from auricular cartilage dysplasia and has unfortunate physical and psychological consequences for children. However, existing treatments have adverse outcomes and its pathogenesis is poorly understood. Since characterization of cell type composition and function in normal auricular cartilage can increase our understanding of microtia, we conducted single-cell transcriptomic profiling for 47,969 human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. Comprehensive bioinformatic analysis identified seven cartilage-related cell subtypes belonging to the chondral and stromal lineages. We also found age-associated changes in gene expression shared across all subtypes in the chondral lineage of NC. Additionally, we revealed the previously unrecognized chondral stem/progenitor cells (CSPCs) that were mainly located in the chondrium and might have the potential for directed chondrogenic differentiation. Our results showed that dysregulation of SOX8 and EGR1 in CSPCs of microtia impaired cartilage development and enhanced oxidative stress response, respectively. These findings shed light on the potential mechanisms of microtia pathogenesis and offer novel avenues for the development of treatment strategies Overall design: Single-cell mRNA sequencing of human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. + GSE179135 + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + M3 + + 9606 + Homo sapiens + + + + + bioproject + 742395 + + + + + + + source_name + Microtia3 + + + tissue + auricular cartilage + + + type + microtia + + + age + 10 + + + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + + + + + + SRR14972348 + GSM5410492_r1 + + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972349 + GSM5410492_r2 + + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972351 + GSM5410492_r3 + + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972353 + GSM5410492_r4 + + + + + + SRS9316013 + SAMN19948078 + GSM5410492 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11287785 + + GSM5410491: M2; Homo sapiens; RNA-Seq + + + SRP326057 + + + + + + + SRS9316012 + GSM5410491 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After the perichondrium was stripped on ice immediately, all auricular cartilage samples were minced into ~1 mm2 pieces and digested for 10 minutes with trypsin at 37°C to remove residual tissue attached to cartilage tissue. The cell suspension was loaded onto the Chromium single-cell controller (10x Genomics, USA) to generate single-cell gel beads in the emulsion (GEMs) by using Single Cell 3′ Library and Gel Bead Kit V3 (10x Genomics, USA) and Chromium Single Cell A Chip Kit (10x Genomics, USA) (performed by CapitalBio Technology, Beijing) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305410491 + + + + + + + GEO Accession + GSM5410491 + + + + + + SRA1252149 + GEO: GSE179135 + + + + NCBI + + + Geo + Curators + + + + + + SRP326057 + PRJNA742395 + GSE179135 + + + Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population + + As one of most common birth defects worldwide, microtia results from auricular cartilage dysplasia and has unfortunate physical and psychological consequences for children. However, existing treatments have adverse outcomes and its pathogenesis is poorly understood. Since characterization of cell type composition and function in normal auricular cartilage can increase our understanding of microtia, we conducted single-cell transcriptomic profiling for 47,969 human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. Comprehensive bioinformatic analysis identified seven cartilage-related cell subtypes belonging to the chondral and stromal lineages. We also found age-associated changes in gene expression shared across all subtypes in the chondral lineage of NC. Additionally, we revealed the previously unrecognized chondral stem/progenitor cells (CSPCs) that were mainly located in the chondrium and might have the potential for directed chondrogenic differentiation. Our results showed that dysregulation of SOX8 and EGR1 in CSPCs of microtia impaired cartilage development and enhanced oxidative stress response, respectively. These findings shed light on the potential mechanisms of microtia pathogenesis and offer novel avenues for the development of treatment strategies Overall design: Single-cell mRNA sequencing of human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. + GSE179135 + + + + + SRS9316012 + SAMN19948079 + GSM5410491 + + M2 + + 9606 + Homo sapiens + + + + + bioproject + 742395 + + + + + + + source_name + Microtia2 + + + tissue + auricular cartilage + + + type + microtia + + + age + 10 + + + + + + + SRS9316012 + SAMN19948079 + GSM5410491 + + + + + + + SRR14972342 + GSM5410491_r1 + + + + + + SRS9316012 + SAMN19948079 + GSM5410491 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR14972294 + GSM5410485_r8 + + + + + + SRS9316010 + SAMN19948086 + GSM5410485 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11287778 + + GSM5410484: C1; Homo sapiens; RNA-Seq + + + SRP326057 + + + + + + + SRS9316009 + GSM5410484 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After the perichondrium was stripped on ice immediately, all auricular cartilage samples were minced into ~1 mm2 pieces and digested for 10 minutes with trypsin at 37°C to remove residual tissue attached to cartilage tissue. The cell suspension was loaded onto the Chromium single-cell controller (10x Genomics, USA) to generate single-cell gel beads in the emulsion (GEMs) by using Single Cell 3′ Library and Gel Bead Kit V3 (10x Genomics, USA) and Chromium Single Cell A Chip Kit (10x Genomics, USA) (performed by CapitalBio Technology, Beijing) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305410484 + + + + + + + GEO Accession + GSM5410484 + + + + + + SRA1252149 + GEO: GSE179135 + + + + NCBI + + + Geo + Curators + + + + + + SRP326057 + PRJNA742395 + GSE179135 + + + Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population + + As one of most common birth defects worldwide, microtia results from auricular cartilage dysplasia and has unfortunate physical and psychological consequences for children. However, existing treatments have adverse outcomes and its pathogenesis is poorly understood. Since characterization of cell type composition and function in normal auricular cartilage can increase our understanding of microtia, we conducted single-cell transcriptomic profiling for 47,969 human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. Comprehensive bioinformatic analysis identified seven cartilage-related cell subtypes belonging to the chondral and stromal lineages. We also found age-associated changes in gene expression shared across all subtypes in the chondral lineage of NC. Additionally, we revealed the previously unrecognized chondral stem/progenitor cells (CSPCs) that were mainly located in the chondrium and might have the potential for directed chondrogenic differentiation. Our results showed that dysregulation of SOX8 and EGR1 in CSPCs of microtia impaired cartilage development and enhanced oxidative stress response, respectively. These findings shed light on the potential mechanisms of microtia pathogenesis and offer novel avenues for the development of treatment strategies Overall design: Single-cell mRNA sequencing of human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. + GSE179135 + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + C1 + + 9606 + Homo sapiens + + + + + bioproject + 742395 + + + + + + + source_name + Normal control1 + + + tissue + auricular cartilage + + + type + normal control + + + age + 42 + + + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + + + + + + SRR14972272 + GSM5410484_r1 + + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972274 + GSM5410484_r2 + + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972276 + GSM5410484_r3 + + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR14972278 + GSM5410484_r4 + + + + + + SRS9316009 + SAMN19948087 + GSM5410484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE180672.xml b/tests/data/GSE180672.xml new file mode 100644 index 0000000..f7a645b --- /dev/null +++ b/tests/data/GSE180672.xml @@ -0,0 +1,3856 @@ + + + + + + + SRX11523992 + + GSM5467484: PS19 Grn-/-_3 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561358 + GSM5467484 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467484 + + + + + + + GEO Accession + GSM5467484 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561358 + SAMN20351486 + GSM5467484 + + PS19 Grn-/-_3 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn-/- + + + + + + + SRS9561358 + SAMN20351486 + GSM5467484 + + + + + + + SRR15218041 + GSM5467484_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=264_MMT_S2_L003_I1_001.fastq.gz --read2PairFiles=264_MMT_S2_L003_R1_001.fastq.gz --read3PairFiles=264_MMT_S2_L003_R2_001.fastq.gz + + + + + + SRS9561358 + SAMN20351486 + GSM5467484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523991 + + GSM5467483: PS19 Grn-/-_2 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561357 + GSM5467483 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467483 + + + + + + + GEO Accession + GSM5467483 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561357 + SAMN20351482 + GSM5467483 + + PS19 Grn-/-_2 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn-/- + + + + + + + SRS9561357 + SAMN20351482 + GSM5467483 + + + + + + + SRR15218040 + GSM5467483_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=231_MMT_S7_L003_I1_001.fastq.gz --read2PairFiles=231_MMT_S7_L003_R1_001.fastq.gz --read3PairFiles=231_MMT_S7_L003_R2_001.fastq.gz + + + + + + SRS9561357 + SAMN20351482 + GSM5467483 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523990 + + GSM5467482: PS19 Grn-/-_1 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561356 + GSM5467482 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467482 + + + + + + + GEO Accession + GSM5467482 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561356 + SAMN20351483 + GSM5467482 + + PS19 Grn-/-_1 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn-/- + + + + + + + SRS9561356 + SAMN20351483 + GSM5467482 + + + + + + + SRR15218039 + GSM5467482_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=215_MMT_S18_L004_I1_001.fastq.gz --read2PairFiles=215_MMT_S18_L004_R1_001.fastq.gz --read3PairFiles=215_MMT_S18_L004_R2_001.fastq.gz + + + + + + SRS9561356 + SAMN20351483 + GSM5467482 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523989 + + GSM5467481: PS19 Grn+/-_3 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561355 + GSM5467481 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467481 + + + + + + + GEO Accession + GSM5467481 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561355 + SAMN20351485 + GSM5467481 + + PS19 Grn+/-_3 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn+/- + + + + + + + SRS9561355 + SAMN20351485 + GSM5467481 + + + + + + + SRR15218038 + GSM5467481_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=272_MMT_S3_L003_I1_001.fastq.gz --read2PairFiles=272_MMT_S3_L003_R1_001.fastq.gz --read3PairFiles=272_MMT_S3_L003_R2_001.fastq.gz + + + + + + SRS9561355 + SAMN20351485 + GSM5467481 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523988 + + GSM5467480: PS19 Grn+/-_2 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561354 + GSM5467480 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467480 + + + + + + + GEO Accession + GSM5467480 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561354 + SAMN20351487 + GSM5467480 + + PS19 Grn+/-_2 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn+/- + + + + + + + SRS9561354 + SAMN20351487 + GSM5467480 + + + + + + + SRR15218037 + GSM5467480_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=260_MMT_S9_L003_I1_001.fastq.gz --read2PairFiles=260_MMT_S9_L003_R1_001.fastq.gz --read3PairFiles=260_MMT_S9_L003_R2_001.fastq.gz + + + + + + SRS9561354 + SAMN20351487 + GSM5467480 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523987 + + GSM5467479: PS19 Grn+/-_1 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561353 + GSM5467479 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467479 + + + + + + + GEO Accession + GSM5467479 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561353 + SAMN20351488 + GSM5467479 + + PS19 Grn+/-_1 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 Grn+/- + + + + + + + SRS9561353 + SAMN20351488 + GSM5467479 + + + + + + + SRR15218036 + GSM5467479_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=211_MMT_S16_L004_I1_001.fastq.gz --read2PairFiles=211_MMT_S16_L004_R1_001.fastq.gz --read3PairFiles=211_MMT_S16_L004_R2_001.fastq.gz + + + + + + SRS9561353 + SAMN20351488 + GSM5467479 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523986 + + GSM5467478: PS19_3 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561352 + GSM5467478 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467478 + + + + + + + GEO Accession + GSM5467478 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561352 + SAMN20351489 + GSM5467478 + + PS19_3 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 + + + + + + + SRS9561352 + SAMN20351489 + GSM5467478 + + + + + + + SRR15218035 + GSM5467478_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=262_MMT_S1_L003_I1_001.fastq.gz --read2PairFiles=262_MMT_S1_L003_R1_001.fastq.gz --read3PairFiles=262_MMT_S1_L003_R2_001.fastq.gz + + + + + + SRS9561352 + SAMN20351489 + GSM5467478 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523985 + + GSM5467477: PS19_2 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561351 + GSM5467477 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467477 + + + + + + + GEO Accession + GSM5467477 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561351 + SAMN20351490 + GSM5467477 + + PS19_2 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 + + + + + + + SRS9561351 + SAMN20351490 + GSM5467477 + + + + + + + SRR15218034 + GSM5467477_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=235_MMT_S8_L003_I1_001.fastq.gz --read2PairFiles=235_MMT_S8_L003_R1_001.fastq.gz --read3PairFiles=235_MMT_S8_L003_R2_001.fastq.gz + + + + + + SRS9561351 + SAMN20351490 + GSM5467477 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523984 + + GSM5467476: PS19_1 hippocampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561350 + GSM5467476 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467476 + + + + + + + GEO Accession + GSM5467476 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561350 + SAMN20351491 + GSM5467476 + + PS19_1 hippocampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + PS19 + + + + + + + SRS9561350 + SAMN20351491 + GSM5467476 + + + + + + + SRR15218033 + GSM5467476_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=214_MMT_S17_L004_I1_001.fastq.gz --read2PairFiles=214_MMT_S17_L004_R1_001.fastq.gz --read3PairFiles=214_MMT_S17_L004_R2_001.fastq.gz + + + + + + SRS9561350 + SAMN20351491 + GSM5467476 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523983 + + GSM5467475: Grn-/-_3 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561349 + GSM5467475 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467475 + + + + + + + GEO Accession + GSM5467475 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561349 + SAMN20351492 + GSM5467475 + + Grn-/-_3 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn-/- + + + + + + + SRS9561349 + SAMN20351492 + GSM5467475 + + + + + + + SRR15218032 + GSM5467475_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=209_MMT_S4_L003_I1_001.fastq.gz --read2PairFiles=209_MMT_S4_L003_R1_001.fastq.gz --read3PairFiles=209_MMT_S4_L003_R2_001.fastq.gz + + + + + + SRS9561349 + SAMN20351492 + GSM5467475 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523982 + + GSM5467474: Grn-/-_2 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561348 + GSM5467474 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467474 + + + + + + + GEO Accession + GSM5467474 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561348 + SAMN20351493 + GSM5467474 + + Grn-/-_2 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn-/- + + + + + + + SRS9561348 + SAMN20351493 + GSM5467474 + + + + + + + SRR15218031 + GSM5467474_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=200_MMT_S10_L003_I1_001.fastq.gz --read2PairFiles=200_MMT_S10_L003_R1_001.fastq.gz --read3PairFiles=200_MMT_S10_L003_R2_001.fastq.gz + + + + + + SRS9561348 + SAMN20351493 + GSM5467474 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523981 + + GSM5467473: Grn-/-_1 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561346 + GSM5467473 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467473 + + + + + + + GEO Accession + GSM5467473 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561346 + SAMN20351496 + GSM5467473 + + Grn-/-_1 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn-/- + + + + + + + SRS9561346 + SAMN20351496 + GSM5467473 + + + + + + + SRR15218030 + GSM5467473_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=198_MMT_S1_L004_I1_001.fastq.gz --read2PairFiles=198_MMT_S1_L004_R1_001.fastq.gz --read3PairFiles=198_MMT_S1_L004_R2_001.fastq.gz + + + + + + SRS9561346 + SAMN20351496 + GSM5467473 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523980 + + GSM5467472: Grn+/-_3 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561347 + GSM5467472 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467472 + + + + + + + GEO Accession + GSM5467472 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561347 + SAMN20351498 + GSM5467472 + + Grn+/-_3 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn+/- + + + + + + + SRS9561347 + SAMN20351498 + GSM5467472 + + + + + + + SRR15218029 + GSM5467472_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=257_MMT_S5_L003_I1_001.fastq.gz --read2PairFiles=257_MMT_S5_L003_R1_001.fastq.gz --read3PairFiles=257_MMT_S5_L003_R2_001.fastq.gz + + + + + + SRS9561347 + SAMN20351498 + GSM5467472 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523979 + + GSM5467471: Grn+/-_2 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561345 + GSM5467471 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467471 + + + + + + + GEO Accession + GSM5467471 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561345 + SAMN20351500 + GSM5467471 + + Grn+/-_2 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn+/- + + + + + + + SRS9561345 + SAMN20351500 + GSM5467471 + + + + + + + SRR15218028 + GSM5467471_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=232_MMT_S12_L004_I1_001.fastq.gz --read2PairFiles=232_MMT_S12_L004_R1_001.fastq.gz --read3PairFiles=232_MMT_S12_L004_R2_001.fastq.gz + + + + + + SRS9561345 + SAMN20351500 + GSM5467471 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523978 + + GSM5467470: Grn+/-_1 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561344 + GSM5467470 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467470 + + + + + + + GEO Accession + GSM5467470 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561344 + SAMN20351501 + GSM5467470 + + Grn+/-_1 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + Grn+/- + + + + + + + SRS9561344 + SAMN20351501 + GSM5467470 + + + + + + + SRR15218027 + GSM5467470_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=207_MMT_S14_L004_I1_001.fastq.gz --read2PairFiles=207_MMT_S14_L004_R1_001.fastq.gz --read3PairFiles=207_MMT_S14_L004_R2_001.fastq.gz + + + + + + SRS9561344 + SAMN20351501 + GSM5467470 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523977 + + GSM5467469: WT_3 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561343 + GSM5467469 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467469 + + + + + + + GEO Accession + GSM5467469 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561343 + SAMN20351467 + GSM5467469 + + WT_3 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + WT + + + + + + + SRS9561343 + SAMN20351467 + GSM5467469 + + + + + + + SRR15218026 + GSM5467469_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=258_MMT_S6_L003_I1_001.fastq.gz --read2PairFiles=258_MMT_S6_L003_R1_001.fastq.gz --read3PairFiles=258_MMT_S6_L003_R2_001.fastq.gz + + + + + + SRS9561343 + SAMN20351467 + GSM5467469 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523976 + + GSM5467468: WT_2 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561342 + GSM5467468 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467468 + + + + + + + GEO Accession + GSM5467468 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561342 + SAMN20351469 + GSM5467468 + + WT_2 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + WT + + + + + + + SRS9561342 + SAMN20351469 + GSM5467468 + + + + + + + SRR15218025 + GSM5467468_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=230_MMT_S11_L004_I1_001.fastq.gz --read2PairFiles=230_MMT_S11_L004_R1_001.fastq.gz --read3PairFiles=230_MMT_S11_L004_R2_001.fastq.gz + + + + + + SRS9561342 + SAMN20351469 + GSM5467468 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11523975 + + GSM5467467: WT_1 hippomcampal nuclei; Mus musculus; RNA-Seq + + + SRP329514 + + + + + + + SRS9561341 + GSM5467467 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305467467 + + + + + + + GEO Accession + GSM5467467 + + + + + + SRA1263366 + GEO: GSE180672 + + + + NCBI + + + Geo + Curators + + + + + + SRP329514 + PRJNA749056 + GSE180672 + + + Progranulin–glucocerebrosidase complex regulates tau and alpha-synuclein inclusions to alter phenotypes in tauopathy + + Many neurodegenerative disorders including Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are characterized by abnormal protein deposition and frequently show comorbid pathology. Progranulin (PGRN) is implicated not only in TDP-43 but in tau and alpha-synuclein proteinopathies. However, the underlying mechanisms are unknown. Here, we generated P301S tau transgenic mice with PGRN haploinsufficiency and loss and found that those mice exhibit exacerbated disinhibition phenotype while showing attenuated memory impairment, hippocampal atrophy, and transcriptomic changes. Remarkably, the phenotypic alteration was accompanied by an increase in tau inclusions, which are positive for alpha-synuclein, a PGRN binding partner beta-glucocerebrosidase (GCase), and its substrate glucosylceramide. GCase inhibition or PGRN deficiency enhanced tau aggregation induced by AD-derived tau seeds in neurons. In vitro, GCase and glucosylceramide promoted P301S tau aggregation. Similar co-pathology was observed in AD and FTLD-GRN patients. Overall design: 18 samples (hippocampus) from 6 genotypes with 3 biological replicates were individually processed and sequenced. Nuclei were isolated from hippocampi using Nuclei EZ Prep Kit (SIGMA #NUC-101). Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) . The libraries underwent HiSeq paired-end sequencing with a sequence depth of 200 million reads per sample using NovaSeq instrument (Ilumina). + GSE180672 + + + + + pubmed + 38365772 + + + + + + + SRS9561341 + SAMN20351471 + GSM5467467 + + WT_1 hippomcampal nuclei + + 10090 + Mus musculus + + + + + bioproject + 749056 + + + + + + + source_name + Hippocampal nuclei + + + tissue + Hippocampus + + + strain + B6C3 + + + age + 7 months old + + + genotype + WT + + + + + + + SRS9561341 + SAMN20351471 + GSM5467467 + + + + + + + SRR15218024 + GSM5467467_r1 + + + + + loader + fastq-load.py + + + options + --platform=Illumina --readTypes=TTB --read1PairFiles=208_MMT_S15_L004_I1_001.fastq.gz --read2PairFiles=208_MMT_S15_L004_R1_001.fastq.gz --read3PairFiles=208_MMT_S15_L004_R2_001.fastq.gz + + + + + + SRS9561341 + SAMN20351471 + GSM5467467 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE181021.xml b/tests/data/GSE181021.xml new file mode 100644 index 0000000..ef3687e --- /dev/null +++ b/tests/data/GSE181021.xml @@ -0,0 +1,1884 @@ + + + + + + + SRX11583664 + + GSM5482109: NAc Setd1+/- scRNA-Seq Sample2; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616885 + GSM5482109 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482109 + + + + + + + GEO Accession + GSM5482109 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616885 + SAMN20457254 + GSM5482109 + + NAc Setd1+/- scRNA-Seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + NAc + + + strain + C57BL/6N + + + tissue + NAc + + + Sex + male + + + age + 8-10 weeks + + + treatment + Setd1a CRISPR-Cas9 + + + + + + + SRS9616885 + SAMN20457254 + GSM5482109 + + + + + + + SRR15278776 + GSM5482109_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616885 + SAMN20457254 + GSM5482109 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11583663 + + GSM5482108: NAc Setd1+/- scRNA-Seq Sample1; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616886 + GSM5482108 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482108 + + + + + + + GEO Accession + GSM5482108 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616886 + SAMN20457253 + GSM5482108 + + NAc Setd1+/- scRNA-Seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + NAc + + + strain + C57BL/6N + + + tissue + NAc + + + Sex + male + + + age + 8-10 weeks + + + treatment + Setd1a CRISPR-Cas9 + + + + + + + SRS9616886 + SAMN20457253 + GSM5482108 + + + + + + + SRR15278775 + GSM5482108_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616886 + SAMN20457253 + GSM5482108 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX11583662 + + GSM5482107: NAc WT scRNA-Seq Sample2; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616884 + GSM5482107 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482107 + + + + + + + GEO Accession + GSM5482107 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616884 + SAMN20457252 + GSM5482107 + + NAc WT scRNA-Seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + NAc + + + strain + C57BL/6N + + + tissue + NAc + + + Sex + male + + + age + 8-10 weeks + + + treatment + None + + + + + + + SRS9616884 + SAMN20457252 + GSM5482107 + + + + + + + SRR15278774 + GSM5482107_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616884 + SAMN20457252 + GSM5482107 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX11583661 + + GSM5482106: NAc WT scRNA-Seq Sample1; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616611 + GSM5482106 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482106 + + + + + + + GEO Accession + GSM5482106 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616611 + SAMN20457251 + GSM5482106 + + NAc WT scRNA-Seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + NAc + + + strain + C57BL/6N + + + tissue + NAc + + + Sex + male + + + age + 8-10 weeks + + + treatment + None + + + + + + + SRS9616611 + SAMN20457251 + GSM5482106 + + + + + + + SRR15278773 + GSM5482106_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616611 + SAMN20457251 + GSM5482106 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX11583660 + + GSM5482105: PFC Setd1+/- scRNA-Seq Sample2; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616609 + GSM5482105 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482105 + + + + + + + GEO Accession + GSM5482105 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616609 + SAMN20457250 + GSM5482105 + + PFC Setd1+/- scRNA-Seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + PFC + + + strain + C57BL/6N + + + tissue + PFC + + + Sex + male + + + age + 8-10 weeks + + + treatment + Setd1a CRISPR-Cas9 + + + + + + + SRS9616609 + SAMN20457250 + GSM5482105 + + + + + + + SRR15278772 + GSM5482105_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616609 + SAMN20457250 + GSM5482105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX11583659 + + GSM5482104: PFC Setd1+/- scRNA-Seq Sample1; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616610 + GSM5482104 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482104 + + + + + + + GEO Accession + GSM5482104 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616610 + SAMN20457249 + GSM5482104 + + PFC Setd1+/- scRNA-Seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + PFC + + + strain + C57BL/6N + + + tissue + PFC + + + Sex + male + + + age + 8-10 weeks + + + treatment + Setd1a CRISPR-Cas9 + + + + + + + SRS9616610 + SAMN20457249 + GSM5482104 + + + + + + + SRR15278771 + GSM5482104_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616610 + SAMN20457249 + GSM5482104 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX11583658 + + GSM5482103: PFC WT scRNA-Seq Sample2; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616607 + GSM5482103 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482103 + + + + + + + GEO Accession + GSM5482103 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616607 + SAMN20457248 + GSM5482103 + + PFC WT scRNA-Seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + PFC + + + strain + C57BL/6N + + + tissue + PFC + + + Sex + male + + + age + 8-10 weeks + + + treatment + None + + + + + + + SRS9616607 + SAMN20457248 + GSM5482103 + + + + + + + SRR15278770 + GSM5482103_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616607 + SAMN20457248 + GSM5482103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX11583657 + + GSM5482102: PFC WT scRNA-Seq Sample1; Mus musculus; RNA-Seq + + + SRP330232 + + + + + + + SRS9616608 + GSM5482102 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion. The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp). + + + + + Illumina HiSeq 2500 + + + + + + gds + 305482102 + + + + + + + GEO Accession + GSM5482102 + + + + + + SRA1266173 + GEO: GSE181021 + + + + NCBI + + + Geo + Curators + + + + + + SRP330232 + PRJNA750436 + GSE181021 + + + Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [single-cell RNA-seq] + + Schizophrenia (SCZ) is a chronic, serious mental disorder with severe burden on patients' families and society. Although over 100 genes have been linked to SCZ pathogenies, the underlying molecular and cellular mechanisms remain largely unknown. Here, we generated a Setd1a haploinsufficiency mouse model to understand how this SCZ-associated epigenetic factor affects gene expression programs in cells of brain regions highly relevant to SCZ. By comparing single-cell RNA-seq results from wild type and Setd1a+/- mice, we found Setd1a heterozygosity causes highly diverse transcriptional adaptations across different cell types in prefrontal cortex and striatum, suggesting brain region- and cell type-specific mechanisms contribute to pathophysiology of SCZ. Interestingly, we found the Foxp2+ neurons exhibit the most prominent gene expression changes among the different neuron subtypes in PFC, which correlate with the H3K4me3 changes. Importantly, many of the genes dysregulated in heterozygous Setd1a mice are linked to neuron morphogenesis and synaptic function. Consistently, heterozygous Setd1a mice exhibit certain behavioral features of SCZ patients. Collectively, our study establishes Setd1a heterozygous mice as a model for understanding SCZ and uncovers a complex brain region- and cell type-specific changes that potentially underlying SCZ pathogenesis. Overall design: To mimic Setd1a loss-of-function mutations in a mouse model, we used CRISPR-Cas9 technique and targeted the 15th exon of Setd1a , which is right before the SET domain encoded by exons 16-18. we dissected PFC tissues from acute coronal sections of Setd1a+/- and WT mouse brains and dissociated the tissues to single cells, which were processed with the 10x Chromium platform (10X Genomics, CA). In additional to PFC, we performed similar scRNA-seq to analyze the transcriptional effect of Setd1a heterozygosity in striatum (including both dorsal and ventral striatum) of two WT and two Setd1a+/- mice. + GSE181021 + + + + + pubmed + 35245111 + + + + + + parent_bioproject + PRJNA750428 + + + + + + SRS9616608 + SAMN20457246 + GSM5482102 + + PFC WT scRNA-Seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 750436 + + + + + + + source_name + PFC + + + strain + C57BL/6N + + + tissue + PFC + + + Sex + male + + + age + 8-10 weeks + + + treatment + None + + + + + + + SRS9616608 + SAMN20457246 + GSM5482102 + + + + + + + SRR15278769 + GSM5482102_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS9616608 + SAMN20457246 + GSM5482102 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE181989.xml b/tests/data/GSE181989.xml new file mode 100644 index 0000000..2b30408 --- /dev/null +++ b/tests/data/GSE181989.xml @@ -0,0 +1,1888 @@ + + + + + + + SRX11729091 + + GSM5515744: BM sample, healthy donor2; Homo sapiens; RNA-Seq + + + SRP332279 + + + + + + + SRS9757828 + GSM5515744 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Ki according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305515744 + + + + + + + GEO Accession + GSM5515744 + + + + + + SRA1277310 + GEO: GSE181989 + + + + NCBI + + + Geo + Curators + + + + + + SRP332279 + PRJNA754149 + GSE181989 + + + Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation kit according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. Overall design: a large-scale single-cell transcriptomic sequencing of 20,000 bone marrow cells from two adult healthy donors and two AA patients + GSE181989 + + + + + pubmed + 35046994 + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + BM sample, healthy donor2 + + 9606 + Homo sapiens + + + + + bioproject + 754149 + + + + + + + source_name + BM sample, healthy donor2 + + + disease state + control + + + tissue + bone marrow + + + cell type + mixed sample (MNCs were mixed with CD34+ cells in a ratio of 4:1) + + + treatment + untreated + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + + + + + + SRR15427722 + GSM5515744_r1 + + + + + loader + fastq-load.py + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427723 + GSM5515744_r2 + + + + + loader + fastq-load.py + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427724 + GSM5515744_r3 + + + + + loader + fastq-load.py + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427725 + GSM5515744_r4 + + + + + loader + fastq-load.py + + + + + + + SRS9757828 + SAMN20745955 + GSM5515744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11729090 + + GSM5515743: BM sample, healthy donor1; Homo sapiens; RNA-Seq + + + SRP332279 + + + + + + + SRS9757827 + GSM5515743 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Ki according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305515743 + + + + + + + GEO Accession + GSM5515743 + + + + + + SRA1277310 + GEO: GSE181989 + + + + NCBI + + + Geo + Curators + + + + + + SRP332279 + PRJNA754149 + GSE181989 + + + Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation kit according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. Overall design: a large-scale single-cell transcriptomic sequencing of 20,000 bone marrow cells from two adult healthy donors and two AA patients + GSE181989 + + + + + pubmed + 35046994 + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + BM sample, healthy donor1 + + 9606 + Homo sapiens + + + + + bioproject + 754149 + + + + + + + source_name + BM sample, healthy donor1 + + + disease state + control + + + tissue + bone marrow + + + cell type + mixed sample (MNCs were mixed with CD34+ cells in a ratio of 4:1) + + + treatment + untreated + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + + + + + + SRR15427714 + GSM5515743_r1 + + + + + loader + fastq-load.py + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR15427719 + GSM5515743_r6 + + + + + loader + fastq-load.py + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427720 + GSM5515743_r7 + + + + + loader + fastq-load.py + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427721 + GSM5515743_r8 + + + + + loader + fastq-load.py + + + + + + + SRS9757827 + SAMN20745954 + GSM5515743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11729089 + + GSM5515742: BM sample, AA patient2; Homo sapiens; RNA-Seq + + + SRP332279 + + + + + + + SRS9757826 + GSM5515742 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Ki according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305515742 + + + + + + + GEO Accession + GSM5515742 + + + + + + SRA1277310 + GEO: GSE181989 + + + + NCBI + + + Geo + Curators + + + + + + SRP332279 + PRJNA754149 + GSE181989 + + + Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation kit according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. Overall design: a large-scale single-cell transcriptomic sequencing of 20,000 bone marrow cells from two adult healthy donors and two AA patients + GSE181989 + + + + + pubmed + 35046994 + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + BM sample, AA patient2 + + 9606 + Homo sapiens + + + + + bioproject + 754149 + + + + + + + source_name + BM sample, AA patient2 + + + disease state + aplastic anemia + + + tissue + bone marrow + + + cell type + mixed sample (MNCs were mixed with CD34+ cells in a ratio of 4:1) + + + treatment + untreated + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + + + + + + SRR15427710 + GSM5515742_r1 + + + + + loader + fastq-load.py + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427711 + GSM5515742_r2 + + + + + loader + fastq-load.py + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427712 + GSM5515742_r3 + + + + + loader + fastq-load.py + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427713 + GSM5515742_r4 + + + + + loader + fastq-load.py + + + + + + + SRS9757826 + SAMN20745952 + GSM5515742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX11729088 + + GSM5515741: BM sample, AA patient1; Homo sapiens; RNA-Seq + + + SRP332279 + + + + + + + SRS9757825 + GSM5515741 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Ki according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305515741 + + + + + + + GEO Accession + GSM5515741 + + + + + + SRA1277310 + GEO: GSE181989 + + + + NCBI + + + Geo + Curators + + + + + + SRP332279 + PRJNA754149 + GSE181989 + + + Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor + + BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation kit according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics. Overall design: a large-scale single-cell transcriptomic sequencing of 20,000 bone marrow cells from two adult healthy donors and two AA patients + GSE181989 + + + + + pubmed + 35046994 + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + BM sample, AA patient1 + + 9606 + Homo sapiens + + + + + bioproject + 754149 + + + + + + + source_name + BM sample, AA patient1 + + + disease state + aplastic anemia + + + tissue + bone marrow + + + cell type + mixed sample (MNCs were mixed with CD34+ cells in a ratio of 4:1) + + + treatment + untreated + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + + + + + + SRR15427706 + GSM5515741_r1 + + + + + loader + fastq-load.py + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427707 + GSM5515741_r2 + + + + + loader + fastq-load.py + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427708 + GSM5515741_r3 + + + + + loader + fastq-load.py + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR15427709 + GSM5515741_r4 + + + + + loader + fastq-load.py + + + + + + + SRS9757825 + SAMN20745951 + GSM5515741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE184506.xml b/tests/data/GSE184506.xml new file mode 100644 index 0000000..b6123af --- /dev/null +++ b/tests/data/GSE184506.xml @@ -0,0 +1,8980 @@ + + + + + + + SRX12279500 + + GSM5590446: Sample 21_L48; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253600 + GSM5590446 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590446 + + + + + + + GEO Accession + GSM5590446 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253600 + SAMN21530296 + GSM5590446 + + Sample 21_L48 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 3 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253600 + SAMN21530296 + GSM5590446 + + + + + + + SRR15990948 + GSM5590446_r1 + + + + + + SRS10253600 + SAMN21530296 + GSM5590446 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279499 + + GSM5590445: Sample 19_L46; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253599 + GSM5590445 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590445 + + + + + + + GEO Accession + GSM5590445 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253599 + SAMN21530295 + GSM5590445 + + Sample 19_L46 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 3 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253599 + SAMN21530295 + GSM5590445 + + + + + + + SRR15990947 + GSM5590445_r1 + + + + + + SRS10253599 + SAMN21530295 + GSM5590445 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279498 + + GSM5590444: Sample 18_L45; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253598 + GSM5590444 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590444 + + + + + + + GEO Accession + GSM5590444 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253598 + SAMN21530318 + GSM5590444 + + Sample 18_L45 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253598 + SAMN21530318 + GSM5590444 + + + + + + + SRR15990946 + GSM5590444_r1 + + + + + + SRS10253598 + SAMN21530318 + GSM5590444 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279497 + + GSM5590443: Sample 17_L44; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253597 + GSM5590443 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590443 + + + + + + + GEO Accession + GSM5590443 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253597 + SAMN21530317 + GSM5590443 + + Sample 17_L44 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253597 + SAMN21530317 + GSM5590443 + + + + + + + SRR15990945 + GSM5590443_r1 + + + + + + SRS10253597 + SAMN21530317 + GSM5590443 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279496 + + GSM5590442: Sample 16_L43; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253596 + GSM5590442 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590442 + + + + + + + GEO Accession + GSM5590442 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253596 + SAMN21530316 + GSM5590442 + + Sample 16_L43 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253596 + SAMN21530316 + GSM5590442 + + + + + + + SRR15990944 + GSM5590442_r1 + + + + + + SRS10253596 + SAMN21530316 + GSM5590442 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279495 + + GSM5590441: Sample 15_L42; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253595 + GSM5590441 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590441 + + + + + + + GEO Accession + GSM5590441 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253595 + SAMN21530315 + GSM5590441 + + Sample 15_L42 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.3 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253595 + SAMN21530315 + GSM5590441 + + + + + + + SRR15990943 + GSM5590441_r1 + + + + + + SRS10253595 + SAMN21530315 + GSM5590441 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279494 + + GSM5590440: Sample 14_L41; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253594 + GSM5590440 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590440 + + + + + + + GEO Accession + GSM5590440 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253594 + SAMN21530314 + GSM5590440 + + Sample 14_L41 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.3 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253594 + SAMN21530314 + GSM5590440 + + + + + + + SRR15990942 + GSM5590440_r1 + + + + + + SRS10253594 + SAMN21530314 + GSM5590440 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279493 + + GSM5590439: Sample 13_L40; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253593 + GSM5590439 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590439 + + + + + + + GEO Accession + GSM5590439 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253593 + SAMN21530313 + GSM5590439 + + Sample 13_L40 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.3 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253593 + SAMN21530313 + GSM5590439 + + + + + + + SRR15990941 + GSM5590439_r1 + + + + + + SRS10253593 + SAMN21530313 + GSM5590439 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279492 + + GSM5590438: Sample 12_L39; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253592 + GSM5590438 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590438 + + + + + + + GEO Accession + GSM5590438 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253592 + SAMN21530312 + GSM5590438 + + Sample 12_L39 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253592 + SAMN21530312 + GSM5590438 + + + + + + + SRR15990940 + GSM5590438_r1 + + + + + + SRS10253592 + SAMN21530312 + GSM5590438 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279491 + + GSM5590437: Sample 11_L38; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253591 + GSM5590437 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590437 + + + + + + + GEO Accession + GSM5590437 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253591 + SAMN21530311 + GSM5590437 + + Sample 11_L38 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253591 + SAMN21530311 + GSM5590437 + + + + + + + SRR15990939 + GSM5590437_r1 + + + + + + SRS10253591 + SAMN21530311 + GSM5590437 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279490 + + GSM5590436: Sample 10_L37; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253590 + GSM5590436 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590436 + + + + + + + GEO Accession + GSM5590436 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253590 + SAMN21530310 + GSM5590436 + + Sample 10_L37 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.1 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253590 + SAMN21530310 + GSM5590436 + + + + + + + SRR15990938 + GSM5590436_r1 + + + + + + SRS10253590 + SAMN21530310 + GSM5590436 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279489 + + GSM5590435: Sample 9_L36; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253589 + GSM5590435 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590435 + + + + + + + GEO Accession + GSM5590435 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253589 + SAMN21530309 + GSM5590435 + + Sample 9_L36 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.03 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253589 + SAMN21530309 + GSM5590435 + + + + + + + SRR15990937 + GSM5590435_r1 + + + + + + SRS10253589 + SAMN21530309 + GSM5590435 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279488 + + GSM5590434: Sample 8_L35; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253588 + GSM5590434 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590434 + + + + + + + GEO Accession + GSM5590434 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253588 + SAMN21530308 + GSM5590434 + + Sample 8_L35 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.03 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253588 + SAMN21530308 + GSM5590434 + + + + + + + SRR15990936 + GSM5590434_r1 + + + + + + SRS10253588 + SAMN21530308 + GSM5590434 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279487 + + GSM5590433: Sample 6_L33; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253587 + GSM5590433 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590433 + + + + + + + GEO Accession + GSM5590433 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253587 + SAMN21530307 + GSM5590433 + + Sample 6_L33 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.01 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253587 + SAMN21530307 + GSM5590433 + + + + + + + SRR15990935 + GSM5590433_r1 + + + + + + SRS10253587 + SAMN21530307 + GSM5590433 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279486 + + GSM5590432: Sample 5_L32; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253586 + GSM5590432 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590432 + + + + + + + GEO Accession + GSM5590432 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253586 + SAMN21530306 + GSM5590432 + + Sample 5_L32 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0.01 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253586 + SAMN21530306 + GSM5590432 + + + + + + + SRR15990934 + GSM5590432_r1 + + + + + + SRS10253586 + SAMN21530306 + GSM5590432 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279485 + + GSM5590431: Sample 3_L30; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253585 + GSM5590431 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590431 + + + + + + + GEO Accession + GSM5590431 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253585 + SAMN21530305 + GSM5590431 + + Sample 3_L30 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253585 + SAMN21530305 + GSM5590431 + + + + + + + SRR15990933 + GSM5590431_r1 + + + + + + SRS10253585 + SAMN21530305 + GSM5590431 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279484 + + GSM5590430: Sample 2_L29; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253584 + GSM5590430 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590430 + + + + + + + GEO Accession + GSM5590430 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253584 + SAMN21530304 + GSM5590430 + + Sample 2_L29 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253584 + SAMN21530304 + GSM5590430 + + + + + + + SRR15990932 + GSM5590430_r1 + + + + + + SRS10253584 + SAMN21530304 + GSM5590430 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279483 + + GSM5590429: Sample 1_L28; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253583 + GSM5590429 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590429 + + + + + + + GEO Accession + GSM5590429 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253583 + SAMN21530303 + GSM5590429 + + Sample 1_L28 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 0 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253583 + SAMN21530303 + GSM5590429 + + + + + + + SRR15990931 + GSM5590429_r1 + + + + + + SRS10253583 + SAMN21530303 + GSM5590429 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279482 + + GSM5590452: Sample 27_L54; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253582 + GSM5590452 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590452 + + + + + + + GEO Accession + GSM5590452 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253582 + SAMN21530302 + GSM5590452 + + Sample 27_L54 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 30 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253582 + SAMN21530302 + GSM5590452 + + + + + + + SRR15990954 + GSM5590452_r1 + + + + + + SRS10253582 + SAMN21530302 + GSM5590452 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279481 + + GSM5590451: Sample 26_L53; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253581 + GSM5590451 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590451 + + + + + + + GEO Accession + GSM5590451 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253581 + SAMN21530301 + GSM5590451 + + Sample 26_L53 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 30 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253581 + SAMN21530301 + GSM5590451 + + + + + + + SRR15990953 + GSM5590451_r1 + + + + + + SRS10253581 + SAMN21530301 + GSM5590451 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279480 + + GSM5590450: Sample 25_L52; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253580 + GSM5590450 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590450 + + + + + + + GEO Accession + GSM5590450 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253580 + SAMN21530300 + GSM5590450 + + Sample 25_L52 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 30 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253580 + SAMN21530300 + GSM5590450 + + + + + + + SRR15990952 + GSM5590450_r1 + + + + + + SRS10253580 + SAMN21530300 + GSM5590450 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279479 + + GSM5590449: Sample 24_L51; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253579 + GSM5590449 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590449 + + + + + + + GEO Accession + GSM5590449 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253579 + SAMN21530299 + GSM5590449 + + Sample 24_L51 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 10 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253579 + SAMN21530299 + GSM5590449 + + + + + + + SRR15990951 + GSM5590449_r1 + + + + + + SRS10253579 + SAMN21530299 + GSM5590449 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279478 + + GSM5590448: Sample 23_L50; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253578 + GSM5590448 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590448 + + + + + + + GEO Accession + GSM5590448 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253578 + SAMN21530298 + GSM5590448 + + Sample 23_L50 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 10 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253578 + SAMN21530298 + GSM5590448 + + + + + + + SRR15990950 + GSM5590448_r1 + + + + + + SRS10253578 + SAMN21530298 + GSM5590448 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX12279477 + + GSM5590447: Sample 22_L49; Mus musculus; RNA-Seq + + + SRP338030 + + + + + + + SRS10253577 + GSM5590447 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle. Libraries were prepared using the 10X Genomics Chromium Single Cell 3' v3.1 kit (10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + gds + 305590447 + + + + + + + GEO Accession + GSM5590447 + + + + + + SRA1297814 + GEO: GSE184506 + + + + NCBI + + + Geo + Curators + + + + + + SRP338030 + PRJNA764849 + GSE184506 + + + Dose-response hepatic single nuclei RNA sequencing of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice + + Dose-response is the cornerstone of safety assessments to determine risk. Innovations in transcriptomic technologies has recently led to the ability to profile gene expression at the single-cell level, enabling comprehensive assessment of adaptive and adverse responses at unprecedented resolution. To demonstrate its application of dose dependent study designs, we performed single nuclei sequencing of livers from male C57BL/6 mice gavaged with the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at doses of 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg or sesame oil vehicle. Following quality control, a total of 131,613 nuclei were sequenced representing 11 distinct cell (sub)types. Our findings reveal dose-dependent changes in relative levels of distinct cell (sub)types such as hepatocytes and macrophages, including the emergence of NASH-associated macrophages (NAMs) characterized by elevated Gpnmb expression. Zonally resolved hepatocytes could also be characterized demonstrating initial induction of aryl hydrocarbon receptor (AhR) target genes such as Cyp1a1 in the central region of the liver lobule while central and portal induction is observed at higher doses. Moreover, we show that zero-inflation inherent to single-cell technologies pose challenges for dose-dependent differential expression analysis and present a novel single-cell Bayesian test method that outperforms common two-group test methods. Collectively, our results demonstrate that single-cell technology can be used to further elucidate mechanisms associated within specific-cell (sub)types and interactions between different cell (sub)types to support the risk assessment paradigm. Overall design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2-3) were orally gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) liver samples were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen liver samples, stained with DAPI, and subjected to FACS to generate a single nuclei suspension. Libraries were prepared using the 10X Genomics Single Cell 3' v3.1 kit. + GSE184506 + + + + + pubmed + 35061903 + + + + + pubmed + 37602218 + + + + + pubmed + 39484576 + + + + + pubmed + 40676134 + + + + + + + SRS10253577 + SAMN21530297 + GSM5590447 + + Sample 22_L49 + + 10090 + Mus musculus + + + + + bioproject + 764849 + + + + + + + source_name + Liver + + + source_ontology + UBERON:0002107 + + + organism_ontology + NCBITAXON:10090 + + + strain + C57BL/6 + + + strain_ontology + MGI:2159769 + + + Sex + male + + + sex_ontology + PATO:0000384 + + + start_age + 28 + + + end_age + 56 + + + age_unit + day + + + age_unit_ontology + UO:0000033 + + + housing_temperature + 23 + + + temperature_unit + degree celsius + + + temperature_unit_ontology + UO:0000027 + + + housing_humidity + 35 + + + humidity_unit + percent + + + humidity_unit_ontology + UO:0000187 + + + light_cycle + 12:12 + + + cage_type + Innovive cage + + + bedding + ALHPA-dri (Shepherd Specialty Papers) + + + water + Aquavive water (Innovive) + + + feed_description + Harlan Teklad 22/5 Rodent Diet 8940 + + + feed_source + Harlan Teklad + + + feed_catalog_no + 8940 + + + toxic_substance + 2,3,7,8-tetrachlorodibenzodioxine + + + toxic_substance_ontology + CHEBI:28119 + + + vendor + Accustandard + + + catalog_number + D-404N + + + toxic_substance_purity + 99.8 + + + vehicle_substance + sesame oil + + + vehicle_substance_ontology + NCIT:C66537 + + + administration_interval + 4 + + + administration_interval_unit + day + + + administration_interval_unit_ontology + UO:0000033 + + + administration_number + 7 + + + administration_route + oral gavage + + + administration_route_ontology + XCO:0000581 + + + dose + 10 + + + dose_unit + microgram per kilogram + + + dose_unit_ontology + EFO:0002899 + + + time_point + 28 + + + time_point_unit + day + + + time_point_unit_ontology + UO:0000033 + + + library_kit + 10X Genomics Chromium Single Cell 3' v3 kit + + + + + + + SRS10253577 + SAMN21530297 + GSM5590447 + + + + + + + SRR15990949 + GSM5590447_r1 + + + + + + SRS10253577 + SAMN21530297 + GSM5590447 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE196929.xml b/tests/data/GSE196929.xml new file mode 100644 index 0000000..991e66d --- /dev/null +++ b/tests/data/GSE196929.xml @@ -0,0 +1,1449 @@ + + + + + + + SRX14206770 + GSM5904835_r1 + + GSM5904835: Mouse 5 at 10 days IRI; Mus musculus; RNA-Seq + + + SRP360241 + PRJNA807744 + + + + + + + SRS12028843 + GSM5904835 + + + + GSM5904835 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + 10x Genomics Single Cell 3′ v3.1 Kit + + + + + Illumina NovaSeq 6000 + + + + + + SRA1374384 + SUB11097514 + + + + Cancer Institute, Cedars Sinai Medical Center + +
+ 8723 Alden Dr. + Los Angeles + CA + USA +
+ + AGCT + Core + + + + + + SRP360241 + PRJNA807744 + GSE196929 + + + Injured Mouse Kidney + + Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing Overall design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury. + GSE196929 + + + + + pubmed + 38386758 + + + + + + + SRS12028843 + SAMN26000623 + GSM5904835 + + Mouse 5 at 10 days IRI + + 10090 + Mus musculus + + + + + bioproject + 807744 + + + + + + + source_name + Mouse Kidney + + + time point + d10 + + + tissue + kidney + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS12028843 + SAMN26000623 + GSM5904835 + + + + + + + SRR18054749 + GSM5904835_r1 + + + + GSM5904835_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028843 + SAMN26000623 + GSM5904835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18054750 + GSM5904835_r2 + + + + GSM5904835_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028843 + SAMN26000623 + GSM5904835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14206769 + GSM5904834_r1 + + GSM5904834: Mouse 4 at 10 days IRI; Mus musculus; RNA-Seq + + + SRP360241 + PRJNA807744 + + + + + + + SRS12028842 + GSM5904834 + + + + GSM5904834 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + 10x Genomics Single Cell 3′ v3.1 Kit + + + + + Illumina NovaSeq 6000 + + + + + + SRA1374384 + SUB11097514 + + + + Cancer Institute, Cedars Sinai Medical Center + +
+ 8723 Alden Dr. + Los Angeles + CA + USA +
+ + AGCT + Core + + + + + + SRP360241 + PRJNA807744 + GSE196929 + + + Injured Mouse Kidney + + Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing Overall design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury. + GSE196929 + + + + + pubmed + 38386758 + + + + + + + SRS12028842 + SAMN26000624 + GSM5904834 + + Mouse 4 at 10 days IRI + + 10090 + Mus musculus + + + + + bioproject + 807744 + + + + + + + source_name + Mouse Kidney + + + time point + d10 + + + tissue + kidney + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS12028842 + SAMN26000624 + GSM5904834 + + + + + + + SRR18054751 + GSM5904834_r1 + + + + GSM5904834_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028842 + SAMN26000624 + GSM5904834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18054752 + GSM5904834_r2 + + + + GSM5904834_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028842 + SAMN26000624 + GSM5904834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14206768 + GSM5904833_r1 + + GSM5904833: Mouse 3 at 10 days IRI; Mus musculus; RNA-Seq + + + SRP360241 + PRJNA807744 + + + + + + + SRS12028841 + GSM5904833 + + + + GSM5904833 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + 10x Genomics Single Cell 3′ v3.1 Kit + + + + + Illumina NovaSeq 6000 + + + + + + SRA1374384 + SUB11097514 + + + + Cancer Institute, Cedars Sinai Medical Center + +
+ 8723 Alden Dr. + Los Angeles + CA + USA +
+ + AGCT + Core + + + + + + SRP360241 + PRJNA807744 + GSE196929 + + + Injured Mouse Kidney + + Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing Overall design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury. + GSE196929 + + + + + pubmed + 38386758 + + + + + + + SRS12028841 + SAMN26000625 + GSM5904833 + + Mouse 3 at 10 days IRI + + 10090 + Mus musculus + + + + + bioproject + 807744 + + + + + + + source_name + Mouse Kidney + + + time point + d10 + + + tissue + kidney + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS12028841 + SAMN26000625 + GSM5904833 + + + + + + + SRR18054753 + GSM5904833_r1 + + + + GSM5904833_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028841 + SAMN26000625 + GSM5904833 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18054754 + GSM5904833_r2 + + + + GSM5904833_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028841 + SAMN26000625 + GSM5904833 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14206767 + GSM5904832_r1 + + GSM5904832: Mouse 2 at 48 hours IRI; Mus musculus; RNA-Seq + + + SRP360241 + PRJNA807744 + + + + + + + SRS12028840 + GSM5904832 + + + + GSM5904832 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + 10x Genomics Single Cell 3′ v3.1 Kit + + + + + Illumina NovaSeq 6000 + + + + + + SRA1374384 + SUB11097514 + + + + Cancer Institute, Cedars Sinai Medical Center + +
+ 8723 Alden Dr. + Los Angeles + CA + USA +
+ + AGCT + Core + + + + + + SRP360241 + PRJNA807744 + GSE196929 + + + Injured Mouse Kidney + + Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing Overall design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury. + GSE196929 + + + + + pubmed + 38386758 + + + + + + + SRS12028840 + SAMN26000626 + GSM5904832 + + Mouse 2 at 48 hours IRI + + 10090 + Mus musculus + + + + + bioproject + 807744 + + + + + + + source_name + Mouse Kidney + + + time point + 48h + + + tissue + kidney + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS12028840 + SAMN26000626 + GSM5904832 + + + + + + + SRR18054755 + GSM5904832_r1 + + + + GSM5904832_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028840 + SAMN26000626 + GSM5904832 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18054756 + GSM5904832_r2 + + + + GSM5904832_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028840 + SAMN26000626 + GSM5904832 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14206766 + GSM5904831_r1 + + GSM5904831: Mouse 1 at 48 hours IRI; Mus musculus; RNA-Seq + + + SRP360241 + PRJNA807744 + + + + + + + SRS12028839 + GSM5904831 + + + + GSM5904831 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + 10x Genomics Single Cell 3′ v3.1 Kit + + + + + Illumina NovaSeq 6000 + + + + + + SRA1374384 + SUB11097514 + + + + Cancer Institute, Cedars Sinai Medical Center + +
+ 8723 Alden Dr. + Los Angeles + CA + USA +
+ + AGCT + Core + + + + + + SRP360241 + PRJNA807744 + GSE196929 + + + Injured Mouse Kidney + + Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing Overall design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury. + GSE196929 + + + + + pubmed + 38386758 + + + + + + + SRS12028839 + SAMN26000627 + GSM5904831 + + Mouse 1 at 48 hours IRI + + 10090 + Mus musculus + + + + + bioproject + 807744 + + + + + + + source_name + Mouse Kidney + + + time point + 48h + + + tissue + kidney + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS12028839 + SAMN26000627 + GSM5904831 + + + + + + + SRR18054757 + GSM5904831_r1 + + + + GSM5904831_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028839 + SAMN26000627 + GSM5904831 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18054758 + GSM5904831_r2 + + + + GSM5904831_r1 + + + + + loader + fastq-load.py + + + + + + SRS12028839 + SAMN26000627 + GSM5904831 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE198891.xml b/tests/data/GSE198891.xml new file mode 100644 index 0000000..2fc8466 --- /dev/null +++ b/tests/data/GSE198891.xml @@ -0,0 +1,2296 @@ + + + + + + + SRX14495285 + GSM5959105_r1 + + GSM5959105: GCA-F-59; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294480 + GSM5959105 + + + + GSM5959105 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294480 + SAMN26752598 + GSM5959105 + + GCA-F-59 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Giant cell arteritis + + + gender + female + + + age + 59 + + + + + + + SRS12294480 + SAMN26752598 + GSM5959105 + + + + + + + SRR18360671 + GSM5959105_r1 + + + + GSM5959105_r1 + + + + + + SRS12294480 + SAMN26752598 + GSM5959105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR18360675 + GSM5959105_r4 + + + + GSM5959105_r1 + + + + + + SRS12294480 + SAMN26752598 + GSM5959105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14495284 + GSM5959100_r1 + + GSM5959100: HC-F-71; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294479 + GSM5959100 + + + + GSM5959100 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294479 + SAMN26752603 + GSM5959100 + + HC-F-71 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Healthy controls + + + gender + female + + + age + 71 + + + + + + + SRS12294479 + SAMN26752603 + GSM5959100 + + + + + + + SRR18360674 + GSM5959100_r1 + + + + GSM5959100_r1 + + + + + + SRS12294479 + SAMN26752603 + GSM5959100 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX14495283 + GSM5959101_r1 + + GSM5959101: HC-F-63; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294478 + GSM5959101 + + + + GSM5959101 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294478 + SAMN26752602 + GSM5959101 + + HC-F-63 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Healthy controls + + + gender + female + + + age + 63 + + + + + + + SRS12294478 + SAMN26752602 + GSM5959101 + + + + + + + SRR18360676 + GSM5959101_r1 + + + + GSM5959101_r1 + + + + + + SRS12294478 + SAMN26752602 + GSM5959101 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX14495282 + GSM5959102_r1 + + GSM5959102: HC-F-67; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294477 + GSM5959102 + + + + GSM5959102 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294477 + SAMN26752601 + GSM5959102 + + HC-F-67 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Healthy controls + + + gender + female + + + age + 67 + + + + + + + SRS12294477 + SAMN26752601 + GSM5959102 + + + + + + + SRR18360678 + GSM5959102_r1 + + + + GSM5959102_r1 + + + + + + SRS12294477 + SAMN26752601 + GSM5959102 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR18360685 + GSM5959102_r2 + + + + GSM5959102_r1 + + + + + + SRS12294477 + SAMN26752601 + GSM5959102 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14495281 + GSM5959103_r1 + + GSM5959103: GCA-F-72; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294476 + GSM5959103 + + + + GSM5959103 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294476 + SAMN26752600 + GSM5959103 + + GCA-F-72 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Giant cell arteritis + + + gender + female + + + age + 72 + + + + + + + SRS12294476 + SAMN26752600 + GSM5959103 + + + + + + + SRR18360682 + GSM5959103_r1 + + + + GSM5959103_r1 + + + + + + SRS12294476 + SAMN26752600 + GSM5959103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR18360688 + GSM5959103_r3 + + + + GSM5959103_r1 + + + + + + SRS12294476 + SAMN26752600 + GSM5959103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR18360689 + GSM5959103_r2 + + + + GSM5959103_r1 + + + + + + SRS12294476 + SAMN26752600 + GSM5959103 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX14495280 + GSM5959104_r1 + + GSM5959104: GCA-F-61; Homo sapiens; RNA-Seq + + + SRP364711 + PRJNA817254 + + + + + + + SRS12294475 + GSM5959104 + + + + GSM5959104 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO. Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3' V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1392218 + SUB11225958 + + + + University Medical Center Groningen + +
+ Hanzeplein 1 + Groningen + Netherlands +
+ + Davide + Cinat + + + + + + SRP364711 + PRJNA817254 + GSE198891 + + + Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis + + Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls. Overall design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment. + GSE198891 + + + + + pubmed + 35460236 + + + + + + + SRS12294475 + SAMN26752599 + GSM5959104 + + GCA-F-61 + + 9606 + Homo sapiens + + + + + bioproject + 817254 + + + + + + + source_name + PBMCs + + + disease state + Giant cell arteritis + + + gender + female + + + age + 61 + + + + + + + SRS12294475 + SAMN26752599 + GSM5959104 + + + + + + + SRR18360686 + GSM5959104_r1 + + + + GSM5959104_r1 + + + + + + SRS12294475 + SAMN26752599 + GSM5959104 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + diff --git a/tests/data/GSE202704.xml b/tests/data/GSE202704.xml new file mode 100644 index 0000000..ea72415 --- /dev/null +++ b/tests/data/GSE202704.xml @@ -0,0 +1,10966 @@ + + + + + + + SRX15231448 + + GSM6131609: S32P; Mus musculus; RNA-Seq + + + SRP374656 + + + + + + + SRS12964903 + GSM6131609 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Sn protocol: the frozen tissue was homogenized in nuclei lysis buffer (NLB) containing 250mM sucrose, 10mM Tris-HCl, 3 mM MgAc2, 0.1mM EDTA, 0.1% Triton X-100 (Sigma-Aldrich, USA) and 0.2 U/μl RNase Inhibitor (Takara, Japan). Tissues were homogenized using a tissue grinder for 15-30 strokes at 2-8°C until they were lysed uniformly. Sucrose concentration was adjusted to purify the nucleus better. sc-RNA Seq sample concentration was adjusted to ~1000 nuclei/μl.single nucleus were collected using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3.1 Reagent Kits (10X Genomics, Pleasanton, USA) . RNA libraries were prepared for sequencing using standard Illumina protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306131609 + + + + + + + GEO Accession + GSM6131609 + + + + + + SRA1418371 + GEO: GSE202704 + + + + NCBI + + + Geo + Curators + + + + + + SRP374656 + PRJNA837074 + GSE202704 + + + snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice + + We performed high-throughput snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice (Mus musculus) to identify cell-type specific differentially expressed genes. Mice were divided into GF, SPF and CGF group. Overall design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from Hip and PFC of 3 GF mice, 3 SPF mice and 3 CGF mice at 8 week old. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3' Reagent Kits v2. Paired-end sequencing was performed on theIllumina NovaSeq 6000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count. + GSE202704 + + + + + pubmed + 36914812 + + + + + + + SRS12964903 + SAMN28188836 + GSM6131609 + + S32P + + 10090 + Mus musculus + + + + + bioproject + 837074 + + + + + + + source_name + Prefrontal cortex + + + strain + SPF + + + tissue/cell type + Prefrontal cortex cells + + + molecule subtype + single-cell nucleus RNA + + + + + + + SRS12964903 + SAMN28188836 + GSM6131609 + + + + + + + SRR19165211 + GSM6131609_r1 + + + + + + SRS12964903 + SAMN28188836 + GSM6131609 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX15231447 + + GSM6131608: S31P; Mus musculus; RNA-Seq + + + SRP374656 + + + + + + + SRS12964902 + GSM6131608 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Sn protocol: the frozen tissue was homogenized in nuclei lysis buffer (NLB) containing 250mM sucrose, 10mM Tris-HCl, 3 mM MgAc2, 0.1mM EDTA, 0.1% Triton X-100 (Sigma-Aldrich, USA) and 0.2 U/μl RNase Inhibitor (Takara, Japan). Tissues were homogenized using a tissue grinder for 15-30 strokes at 2-8°C until they were lysed uniformly. Sucrose concentration was adjusted to purify the nucleus better. sc-RNA Seq sample concentration was adjusted to ~1000 nuclei/μl.single nucleus were collected using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3.1 Reagent Kits (10X Genomics, Pleasanton, USA) . RNA libraries were prepared for sequencing using standard Illumina protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306131608 + + + + + + + GEO Accession + GSM6131608 + + + + + + SRA1418371 + GEO: GSE202704 + + + + NCBI + + + Geo + Curators + + + + + + SRP374656 + PRJNA837074 + GSE202704 + + + snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice + + We performed high-throughput snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice (Mus musculus) to identify cell-type specific differentially expressed genes. Mice were divided into GF, SPF and CGF group. Overall design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from Hip and PFC of 3 GF mice, 3 SPF mice and 3 CGF mice at 8 week old. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3' Reagent Kits v2. Paired-end sequencing was performed on theIllumina NovaSeq 6000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count. + GSE202704 + + + + + pubmed + 36914812 + + + + + + + SRS12964902 + SAMN28188835 + GSM6131608 + + S31P + + 10090 + Mus musculus + + + + + bioproject + 837074 + + + + + + + source_name + Prefrontal cortex + + + strain + SPF + + + tissue/cell type + Prefrontal cortex cells + + + molecule subtype + single-cell nucleus RNA + + + + + + + SRS12964902 + SAMN28188835 + GSM6131608 + + + + + + + SRR19165203 + GSM6131608_r1 + + + + + + SRS12964902 + SAMN28188835 + GSM6131608 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX15231431 + + GSM6131592: C17H; Mus musculus; RNA-Seq + + + SRP374656 + + + + + + + SRS12964886 + GSM6131592 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Sn protocol: the frozen tissue was homogenized in nuclei lysis buffer (NLB) containing 250mM sucrose, 10mM Tris-HCl, 3 mM MgAc2, 0.1mM EDTA, 0.1% Triton X-100 (Sigma-Aldrich, USA) and 0.2 U/μl RNase Inhibitor (Takara, Japan). Tissues were homogenized using a tissue grinder for 15-30 strokes at 2-8°C until they were lysed uniformly. Sucrose concentration was adjusted to purify the nucleus better. sc-RNA Seq sample concentration was adjusted to ~1000 nuclei/μl.single nucleus were collected using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3.1 Reagent Kits (10X Genomics, Pleasanton, USA) . RNA libraries were prepared for sequencing using standard Illumina protocols + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306131592 + + + + + + + GEO Accession + GSM6131592 + + + + + + SRA1418371 + GEO: GSE202704 + + + + NCBI + + + Geo + Curators + + + + + + SRP374656 + PRJNA837074 + GSE202704 + + + snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice + + We performed high-throughput snRNA-seq on hippocampus (Hip) and prefrontal lobe cortex (PFC) tissue in mice (Mus musculus) to identify cell-type specific differentially expressed genes. Mice were divided into GF, SPF and CGF group. Overall design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from Hip and PFC of 3 GF mice, 3 SPF mice and 3 CGF mice at 8 week old. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3' Reagent Kits v2. Paired-end sequencing was performed on theIllumina NovaSeq 6000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count. + GSE202704 + + + + + pubmed + 36914812 + + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + C17H + + 10090 + Mus musculus + + + + + bioproject + 837074 + + + + + + + source_name + Hippocampus + + + strain + CGF + + + tissue/cell type + Hippocampus cells + + + molecule subtype + single-cell nucleus RNA + + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + SRR19165075 + GSM6131592_r1 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165076 + GSM6131592_r2 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165077 + GSM6131592_r3 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165078 + GSM6131592_r4 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165079 + GSM6131592_r5 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165080 + GSM6131592_r6 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165081 + GSM6131592_r7 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR19165082 + GSM6131592_r8 + + + + + + SRS12964886 + SAMN28188819 + GSM6131592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE205049.xml b/tests/data/GSE205049.xml new file mode 100644 index 0000000..bb05228 --- /dev/null +++ b/tests/data/GSE205049.xml @@ -0,0 +1,3712 @@ + + + + + + + SRX15494117 + GSM6204608_r1 + + GSM6204608: Patinet 9 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209217 + GSM6204608 + + + + GSM6204608 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209217 + SAMN28741189 + GSM6204608 + + Patinet 9 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209217 + SAMN28741189 + GSM6204608 + + + + + + + SRR19440920 + GSM6204608_r1 + + + + GSM6204608_r1 + + + + + + SRS13209217 + SAMN28741189 + GSM6204608 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494116 + GSM6204607_r1 + + GSM6204607: Patinet 9 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209216 + GSM6204607 + + + + GSM6204607 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209216 + SAMN28741190 + GSM6204607 + + Patinet 9 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209216 + SAMN28741190 + GSM6204607 + + + + + + + SRR19440921 + GSM6204607_r1 + + + + GSM6204607_r1 + + + + + + SRS13209216 + SAMN28741190 + GSM6204607 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494115 + GSM6204606_r1 + + GSM6204606: Patinet 8 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209215 + GSM6204606 + + + + GSM6204606 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209215 + SAMN28741191 + GSM6204606 + + Patinet 8 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209215 + SAMN28741191 + GSM6204606 + + + + + + + SRR19440922 + GSM6204606_r1 + + + + GSM6204606_r1 + + + + + + SRS13209215 + SAMN28741191 + GSM6204606 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494114 + GSM6204605_r1 + + GSM6204605: Patinet 8 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209214 + GSM6204605 + + + + GSM6204605 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209214 + SAMN28741192 + GSM6204605 + + Patinet 8 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209214 + SAMN28741192 + GSM6204605 + + + + + + + SRR19440923 + GSM6204605_r1 + + + + GSM6204605_r1 + + + + + + SRS13209214 + SAMN28741192 + GSM6204605 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494113 + GSM6204604_r1 + + GSM6204604: Patinet 7 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209213 + GSM6204604 + + + + GSM6204604 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209213 + SAMN28741193 + GSM6204604 + + Patinet 7 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209213 + SAMN28741193 + GSM6204604 + + + + + + + SRR19440924 + GSM6204604_r1 + + + + GSM6204604_r1 + + + + + + SRS13209213 + SAMN28741193 + GSM6204604 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494112 + GSM6204603_r1 + + GSM6204603: Patinet 7 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209212 + GSM6204603 + + + + GSM6204603 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209212 + SAMN28741194 + GSM6204603 + + Patinet 7 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209212 + SAMN28741194 + GSM6204603 + + + + + + + SRR19440925 + GSM6204603_r1 + + + + GSM6204603_r1 + + + + + + SRS13209212 + SAMN28741194 + GSM6204603 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494111 + GSM6204602_r1 + + GSM6204602: Patinet 6 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209211 + GSM6204602 + + + + GSM6204602 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209211 + SAMN28741195 + GSM6204602 + + Patinet 6 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209211 + SAMN28741195 + GSM6204602 + + + + + + + SRR19440926 + GSM6204602_r1 + + + + GSM6204602_r1 + + + + + + SRS13209211 + SAMN28741195 + GSM6204602 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494110 + GSM6204601_r1 + + GSM6204601: Patinet 6 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209210 + GSM6204601 + + + + GSM6204601 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209210 + SAMN28741196 + GSM6204601 + + Patinet 6 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209210 + SAMN28741196 + GSM6204601 + + + + + + + SRR19440927 + GSM6204601_r1 + + + + GSM6204601_r1 + + + + + + SRS13209210 + SAMN28741196 + GSM6204601 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494109 + GSM6204600_r1 + + GSM6204600: Patinet 5 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209208 + GSM6204600 + + + + GSM6204600 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209208 + SAMN28741197 + GSM6204600 + + Patinet 5 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209208 + SAMN28741197 + GSM6204600 + + + + + + + SRR19440928 + GSM6204600_r1 + + + + GSM6204600_r1 + + + + + + SRS13209208 + SAMN28741197 + GSM6204600 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494108 + GSM6204599_r1 + + GSM6204599: Patinet 5 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209209 + GSM6204599 + + + + GSM6204599 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209209 + SAMN28741198 + GSM6204599 + + Patinet 5 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209209 + SAMN28741198 + GSM6204599 + + + + + + + SRR19440929 + GSM6204599_r1 + + + + GSM6204599_r1 + + + + + + SRS13209209 + SAMN28741198 + GSM6204599 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494107 + GSM6204598_r1 + + GSM6204598: Patinet 4 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209206 + GSM6204598 + + + + GSM6204598 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209206 + SAMN28741199 + GSM6204598 + + Patinet 4 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209206 + SAMN28741199 + GSM6204598 + + + + + + + SRR19440930 + GSM6204598_r1 + + + + GSM6204598_r1 + + + + + + SRS13209206 + SAMN28741199 + GSM6204598 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494106 + GSM6204597_r1 + + GSM6204597: Patinet 4 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209205 + GSM6204597 + + + + GSM6204597 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209205 + SAMN28741200 + GSM6204597 + + Patinet 4 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209205 + SAMN28741200 + GSM6204597 + + + + + + + SRR19440931 + GSM6204597_r1 + + + + GSM6204597_r1 + + + + + + SRS13209205 + SAMN28741200 + GSM6204597 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494105 + GSM6204596_r1 + + GSM6204596: Patinet 3 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209204 + GSM6204596 + + + + GSM6204596 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209204 + SAMN28741201 + GSM6204596 + + Patinet 3 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209204 + SAMN28741201 + GSM6204596 + + + + + + + SRR19440932 + GSM6204596_r1 + + + + GSM6204596_r1 + + + + + + SRS13209204 + SAMN28741201 + GSM6204596 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494104 + GSM6204595_r1 + + GSM6204595: Patinet 3 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209203 + GSM6204595 + + + + GSM6204595 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209203 + SAMN28741202 + GSM6204595 + + Patinet 3 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209203 + SAMN28741202 + GSM6204595 + + + + + + + SRR19440933 + GSM6204595_r1 + + + + GSM6204595_r1 + + + + + + SRS13209203 + SAMN28741202 + GSM6204595 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494103 + GSM6204594_r1 + + GSM6204594: Patinet 2 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209207 + GSM6204594 + + + + GSM6204594 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209207 + SAMN28741203 + GSM6204594 + + Patinet 2 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209207 + SAMN28741203 + GSM6204594 + + + + + + + SRR19440934 + GSM6204594_r1 + + + + GSM6204594_r1 + + + + + + SRS13209207 + SAMN28741203 + GSM6204594 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494102 + GSM6204593_r1 + + GSM6204593: Patinet 2 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209202 + GSM6204593 + + + + GSM6204593 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209202 + SAMN28741204 + GSM6204593 + + Patinet 2 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209202 + SAMN28741204 + GSM6204593 + + + + + + + SRR19440935 + GSM6204593_r1 + + + + GSM6204593_r1 + + + + + + SRS13209202 + SAMN28741204 + GSM6204593 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494101 + GSM6204592_r1 + + GSM6204592: Patinet 1 PDAC; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209220 + GSM6204592 + + + + GSM6204592 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209220 + SAMN28741205 + GSM6204592 + + Patinet 1 PDAC + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + PDAC + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209220 + SAMN28741205 + GSM6204592 + + + + + + + SRR19440936 + GSM6204592_r1 + + + + GSM6204592_r1 + + + + + + SRS13209220 + SAMN28741205 + GSM6204592 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX15494100 + GSM6204591_r1 + + GSM6204591: Patinet 1 Adjacent Normal Tissue; Homo sapiens; RNA-Seq + + + SRP377547 + PRJNA843384 + + + + + + + SRS13209201 + GSM6204591 + + + + GSM6204591 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing. Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128) + + + + + Illumina HiSeq 4000 + + + + + + SRA1428748 + SUB11545584 + + + + Universitat Heidelberg + +
+ Im Neuenheimer 672 + Heidelberg + Choose State/Province + Germany +
+ + MENGJIE + QIU + + + + + + SRP377547 + PRJNA843384 + GSE205049 + + + Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer + + As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC that diverge from immune populations within adjacent normal areas, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which explain their differential responsiveness to current immunotherapies, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC. Overall design: mRNA profiles of 9 PDAC and paired adjacent tissues + GSE205049 + + + + + pubmed + 37263303 + + + + + + + SRS13209201 + SAMN28741206 + GSM6204591 + + Patinet 1 Adjacent Normal Tissue + + 9606 + Homo sapiens + + + + + bioproject + 843384 + + + + + + + source_name + Human Pancreatic Biopsy + + + pathology + Adjacent Normal Tissue + + + tissue + Pancreatic + + + treatment + None + + + cell type + CD45+ Single cells from Pancreas + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS13209201 + SAMN28741206 + GSM6204591 + + + + + + + SRR19440937 + GSM6204591_r1 + + + + GSM6204591_r1 + + + + + + SRS13209201 + SAMN28741206 + GSM6204591 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE212351.xml b/tests/data/GSE212351.xml new file mode 100644 index 0000000..e0d29d1 --- /dev/null +++ b/tests/data/GSE212351.xml @@ -0,0 +1,2430 @@ + + + + + + + SRX17360135 + GSM6528457_r1 + + GSM6528457: TS hippocampus, replicate 4, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919540 + GSM6528457 + + + + GSM6528457 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919540 + SAMN30599703 + GSM6528457 + + TS hippocampus, replicate 4, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + TS + + + + + + + SRS14919540 + SAMN30599703 + GSM6528457 + + + + + + + SRR21351994 + GSM6528457_r1 + + + + GSM6528457_r1 + + + + + + SRS14919540 + SAMN30599703 + GSM6528457 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21351996 + GSM6528457_r2 + + + + GSM6528457_r1 + + + + + + SRS14919540 + SAMN30599703 + GSM6528457 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360134 + GSM6528456_r1 + + GSM6528456: TS hippocampus, replicate 3, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919539 + GSM6528456 + + + + GSM6528456 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + TS hippocampus, replicate 3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + TS + + + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + + + + + + SRR21351998 + GSM6528456_r1 + + + + GSM6528456_r1 + + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352000 + GSM6528456_r2 + + + + GSM6528456_r1 + + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352002 + GSM6528456_r3 + + + + GSM6528456_r1 + + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352004 + GSM6528456_r4 + + + + GSM6528456_r1 + + + + + + SRS14919539 + SAMN30599704 + GSM6528456 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360133 + GSM6528455_r1 + + GSM6528455: TS hippocampus, replicate 2, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919538 + GSM6528455 + + + + GSM6528455 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919538 + SAMN30599705 + GSM6528455 + + TS hippocampus, replicate 2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + TS + + + + + + + SRS14919538 + SAMN30599705 + GSM6528455 + + + + + + + SRR21352007 + GSM6528455_r1 + + + + GSM6528455_r1 + + + + + + SRS14919538 + SAMN30599705 + GSM6528455 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352009 + GSM6528455_r2 + + + + GSM6528455_r1 + + + + + + SRS14919538 + SAMN30599705 + GSM6528455 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360132 + GSM6528454_r1 + + GSM6528454: TS hippocampus, replicate 1, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919537 + GSM6528454 + + + + GSM6528454 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919537 + SAMN30599706 + GSM6528454 + + TS hippocampus, replicate 1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + TS + + + + + + + SRS14919537 + SAMN30599706 + GSM6528454 + + + + + + + SRR21352011 + GSM6528454_r1 + + + + GSM6528454_r1 + + + + + + SRS14919537 + SAMN30599706 + GSM6528454 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352013 + GSM6528454_r2 + + + + GSM6528454_r1 + + + + + + SRS14919537 + SAMN30599706 + GSM6528454 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360131 + GSM6528453_r1 + + GSM6528453: WT hippocampus, replicate 4, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919536 + GSM6528453 + + + + GSM6528453 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919536 + SAMN30599707 + GSM6528453 + + WT hippocampus, replicate 4, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + WT + + + + + + + SRS14919536 + SAMN30599707 + GSM6528453 + + + + + + + SRR21352015 + GSM6528453_r1 + + + + GSM6528453_r1 + + + + + + SRS14919536 + SAMN30599707 + GSM6528453 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352017 + GSM6528453_r2 + + + + GSM6528453_r1 + + + + + + SRS14919536 + SAMN30599707 + GSM6528453 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360130 + GSM6528451_r1 + + GSM6528451: WT hippocampus, replicate 2, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919535 + GSM6528451 + + + + GSM6528451 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919535 + SAMN30599709 + GSM6528451 + + WT hippocampus, replicate 2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + WT + + + + + + + SRS14919535 + SAMN30599709 + GSM6528451 + + + + + + + SRR21352019 + GSM6528451_r1 + + + + GSM6528451_r1 + + + + + + SRS14919535 + SAMN30599709 + GSM6528451 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352021 + GSM6528451_r2 + + + + GSM6528451_r1 + + + + + + SRS14919535 + SAMN30599709 + GSM6528451 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360129 + GSM6528452_r1 + + GSM6528452: WT hippocampus, replicate 3, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919534 + GSM6528452 + + + + GSM6528452 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + WT hippocampus, replicate 3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + WT + + + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + + + + + + SRR21352023 + GSM6528452_r1 + + + + GSM6528452_r1 + + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352025 + GSM6528452_r2 + + + + GSM6528452_r1 + + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352027 + GSM6528452_r3 + + + + GSM6528452_r1 + + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352030 + GSM6528452_r4 + + + + GSM6528452_r1 + + + + + + SRS14919534 + SAMN30599708 + GSM6528452 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17360128 + GSM6528450_r1 + + GSM6528450: WT hippocampus, replicate 1, snRNAseq; Mus musculus; RNA-Seq + + + SRP394910 + PRJNA875100 + + + + + + + SRS14919533 + GSM6528450 + + + + GSM6528450 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Each hippocampus was dissected and placed in chilled Hanks' Balanced Salt Solution. The, it was transferred to a new tube containing 500μL chilled EZ Lysis Buffer and homogenized using a sterile RNase-free douncer. The resulting homogenate was filtered using a 70μm strainer mesh to remove remaining chunks of tissue and centrifuged at 500g for 5 minutes at 4ºC. The pellet containing the nuclei was resuspended in 1.5mL EZ Lysis Buffer and centrifuged again. The supernatant was removed and 500μL of Nuclei Wash and Resuspension Buffer (NWRB, 1X PBS, 1% BSA and 0.2U/μL RNase inhibitor) were added without disturbing the pellet and incubated for 5 minutes. After incubation, 1mL of NWRB was added and the pellet resuspended. The nuclei suspension was centrifuged again and the washing step was repeated with 1.5mL of NWRB. After an additional centrifugation, nuclei were resuspended in 500μL of 1:1000 anti-NeuN antibody conjugated with AlexaFluor 647 in PBS and incubated in rotation for 15 minutes at 4ºC. After incubation, nuclei were washed with 500μL of NWRB and centrifuged again. Last, nuclei were resuspended in NWRB supplemented with DAPI and filtered with a 35μm cell strainer to obtain a single-nuclei suspension. Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, 10.000 neuronal nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1488880 + SUB12002057 + + + + Centre for Genomic Regulation (CRG) + +
+ C/ Dr Aiguader 88 + Barcelona + Spain +
+ + Cesar + Sierra + + + + + + SRP394910 + PRJNA875100 + GSE212351 + + + Gene expression profile at single nuclei level of hippocampal neurons from WT and Ts65Dn mice + + In order to characterize the cellular and molecular alterations associated with DS hippocampal dysfunction, given the rich neural cell diversity of this brain region, we used single nucleus RNA sequencing to dissect transcriptional dysregulation associated with specific cell types in the DS mouse model Ts65Dn Overall design: Neuronal hippocampal population from adult (4 month old) mice was isolated by Fluorescence-activated nuclear sorting (FANS) according to the presence or absence of NeuN signal and analyzed using snRNAseq. + GSE212351 + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + WT hippocampus, replicate 1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 875100 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell type + Neurons + + + strain + B6EiC3Sn a/A-Ts(1716)65Dn/J + + + age + 4 month old + + + genotype + WT + + + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + + + + + + SRR21352032 + GSM6528450_r1 + + + + GSM6528450_r1 + + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352034 + GSM6528450_r2 + + + + GSM6528450_r1 + + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352036 + GSM6528450_r3 + + + + GSM6528450_r1 + + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21352038 + GSM6528450_r4 + + + + GSM6528450_r1 + + + + + + SRS14919533 + SAMN30599710 + GSM6528450 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE212505.xml b/tests/data/GSE212505.xml new file mode 100644 index 0000000..5645166 --- /dev/null +++ b/tests/data/GSE212505.xml @@ -0,0 +1,1684 @@ + + + + + + + SRX17392592 + GSM6533799_r1 + + GSM6533799: Control Placenta Site Sample D7; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950990 + GSM6533799 + + + + GSM6533799 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950990 + SAMN30629401 + GSM6533799 + + Control Placenta Site Sample D7 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua + + + tissue + placenta/decidua + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950990 + SAMN30629401 + GSM6533799 + + + + + + + SRR21387194 + GSM6533799_r1 + + + + GSM6533799_r1 + + + + + + SRS14950990 + SAMN30629401 + GSM6533799 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392591 + GSM6533798_r1 + + GSM6533798: Control Placenta Site Sample D3; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950989 + GSM6533798 + + + + GSM6533798 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950989 + SAMN30629402 + GSM6533798 + + Control Placenta Site Sample D3 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua + + + tissue + placenta/decidua + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950989 + SAMN30629402 + GSM6533798 + + + + + + + SRR21387195 + GSM6533798_r1 + + + + GSM6533798_r1 + + + + + + SRS14950989 + SAMN30629402 + GSM6533798 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392590 + GSM6533797_r1 + + GSM6533797: Control Placenta Site Sample D2; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950988 + GSM6533797 + + + + GSM6533797 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950988 + SAMN30629403 + GSM6533797 + + Control Placenta Site Sample D2 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua + + + tissue + placenta/decidua + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950988 + SAMN30629403 + GSM6533797 + + + + + + + SRR21387196 + GSM6533797_r1 + + + + GSM6533797_r1 + + + + + + SRS14950988 + SAMN30629403 + GSM6533797 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392589 + GSM6533796_r1 + + GSM6533796: Accreta Opposite Site Sample D6; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950987 + GSM6533796 + + + + GSM6533796 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950987 + SAMN30629404 + GSM6533796 + + Accreta Opposite Site Sample D6 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua/myometrium + + + tissue + placenta/decidua/myometrium + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950987 + SAMN30629404 + GSM6533796 + + + + + + + SRR21387197 + GSM6533796_r1 + + + + GSM6533796_r1 + + + + + + SRS14950987 + SAMN30629404 + GSM6533796 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392588 + GSM6533795_r1 + + GSM6533795: Accreta Opposite Site Sample D4; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950986 + GSM6533795 + + + + GSM6533795 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950986 + SAMN30629405 + GSM6533795 + + Accreta Opposite Site Sample D4 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua/myometrium + + + tissue + placenta/decidua/myometrium + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950986 + SAMN30629405 + GSM6533795 + + + + + + + SRR21387198 + GSM6533795_r1 + + + + GSM6533795_r1 + + + + + + SRS14950986 + SAMN30629405 + GSM6533795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392587 + GSM6533794_r1 + + GSM6533794: Accreta Invasive Site Sample D6; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950985 + GSM6533794 + + + + GSM6533794 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950985 + SAMN30629406 + GSM6533794 + + Accreta Invasive Site Sample D6 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua/myometrium + + + tissue + placenta/decidua/myometrium + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950985 + SAMN30629406 + GSM6533794 + + + + + + + SRR21387199 + GSM6533794_r1 + + + + GSM6533794_r1 + + + + + + SRS14950985 + SAMN30629406 + GSM6533794 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392586 + GSM6533793_r1 + + GSM6533793: Accreta Invasive Site Sample D5; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950984 + GSM6533793 + + + + GSM6533793 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950984 + SAMN30629407 + GSM6533793 + + Accreta Invasive Site Sample D5 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua/myometrium + + + tissue + placenta/decidua/myometrium + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950984 + SAMN30629407 + GSM6533793 + + + + + + + SRR21387200 + GSM6533793_r1 + + + + GSM6533793_r1 + + + + + + SRS14950984 + SAMN30629407 + GSM6533793 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17392585 + GSM6533792_r1 + + GSM6533792: Accreta Invasive Site Sample D4; Homo sapiens; RNA-Seq + + + SRP395208 + PRJNA875647 + + + + + + + SRS14950983 + GSM6533792 + + + + GSM6533792 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing. scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1494694 + SUB12049402 + + + + Pellegrini Lab, Molecular Biology Institute, UCLA + +
+ 610, Charles Young Dr East, TLSB 3000C + Los Angeles + CA + USA +
+ + Feiyang + Ma + + + + + + SRP395208 + PRJNA875647 + GSE212505 + + + Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease + + This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens. Overall design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants. + GSE212505 + + + + + pubmed + 38296740 + + + + + + + SRS14950983 + SAMN30629408 + GSM6533792 + + Accreta Invasive Site Sample D4 + + 9606 + Homo sapiens + + + + + bioproject + 875647 + + + + + + + source_name + placenta/decidua/myometrium + + + tissue + placenta/decidua/myometrium + + + disease state + third trimester + + + cell type + mixed + + + genotype + NA + + + treatment + NA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14950983 + SAMN30629408 + GSM6533792 + + + + + + + SRR21387201 + GSM6533792_r1 + + + + GSM6533792_r1 + + + + + + SRS14950983 + SAMN30629408 + GSM6533792 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE212527.xml b/tests/data/GSE212527.xml new file mode 100644 index 0000000..16dc1c6 --- /dev/null +++ b/tests/data/GSE212527.xml @@ -0,0 +1,1986 @@ + + + + + + + SRX17394931 + GSM6534013_r1 + + GSM6534013: SRC141; Homo sapiens; RNA-Seq + + + SRP395248 + PRJNA875907 + + + + + + + SRS14953075 + GSM6534013 + + + + GSM6534013 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh tumors were minced and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) using a GentleMACS Octo Dissociator with heaters (Miltenyi Biotec) following the manufacturer's instructions. Libraries were constructed using the Chromium 3' Gene Expression Solution v3.1 (10x Genomics) per the manufacturer's instructions. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1884888 + SUB14494661 + + + + Moding Lab, Radiation Oncology, Stanford University School of Medicine + +
+ 450 Serra Mall + Stanford + CA + USA +
+ + Ajay + Subramanian + + + + + + SRP395248 + PRJNA875907 + GSE212527 + + + Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas. + + The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas. Overall design: Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients. [UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change. + GSE212527 + + + + + pubmed + 38429415 + + + + + + + SRS14953075 + SAMN30631350 + GSM6534013 + + SRC141 + + 9606 + Homo sapiens + + + + + bioproject + 875907 + + + + + + + source_name + Undifferentiated pleomorphic sarcoma + + + tissue + Undifferentiated pleomorphic sarcoma + + + cell type + Tumor + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14953075 + SAMN30631350 + GSM6534013 + + + + + + + SRR21389614 + GSM6534013_r1 + + + + GSM6534013_r1 + + + + + + SRS14953075 + SAMN30631350 + GSM6534013 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 450 Serra Mall + Stanford + CA + USA +
+ + Ajay + Subramanian + + + + + + SRP395248 + PRJNA875907 + GSE212527 + + + Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas. + + The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas. Overall design: Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients. [UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change. + GSE212527 + + + + + pubmed + 38429415 + + + + + + + SRS14953073 + SAMN30631352 + GSM6534011 + + SRC164 + + 9606 + Homo sapiens + + + + + bioproject + 875907 + + + + + + + source_name + Undifferentiated pleomorphic sarcoma + + + tissue + Undifferentiated pleomorphic sarcoma + + + cell type + Tumor + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14953073 + SAMN30631352 + GSM6534011 + + + + + + + SRR21389618 + GSM6534011_r1 + + + + GSM6534011_r1 + + + + + loader + fastq-load.py + + + + + + SRS14953073 + SAMN30631352 + GSM6534011 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX17394935 + GSM6534017_r1 + + GSM6534017: SRC242_pectoralis; Homo sapiens; RNA-Seq + + + SRP395248 + PRJNA875907 + + + + + + + SRS14953079 + GSM6534017 + + + + GSM6534017 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh tumors were minced and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) using a GentleMACS Octo Dissociator with heaters (Miltenyi Biotec) following the manufacturer's instructions. Libraries were constructed using the Chromium 3' Gene Expression Solution v3.1 (10x Genomics) per the manufacturer's instructions. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499884 + SUB12076764 + + + + Moding Lab, Radiation Oncology, Stanford University School of Medicine + +
+ 450 Serra Mall + Stanford + CA + USA +
+ + Ajay + Subramanian + + + + + + SRP395248 + PRJNA875907 + GSE212527 + + + Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas. + + The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas. Overall design: Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients. [UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change. + GSE212527 + + + + + pubmed + 38429415 + + + + + + + SRS14953079 + SAMN30631346 + GSM6534017 + + SRC242_pectoralis + + 9606 + Homo sapiens + + + + + bioproject + 875907 + + + + + + + source_name + Leiomyosarcoma + + + tissue + Leiomyosarcoma + + + cell type + Tumor + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14953079 + SAMN30631346 + GSM6534017 + + + + + + + SRR21389606 + GSM6534017_r1 + + + + GSM6534017_r1 + + + + + loader + fastq-load.py + + + + + + SRS14953079 + SAMN30631346 + GSM6534017 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + Ajay + Subramanian + + + + + + SRP395248 + PRJNA875907 + GSE212527 + + + Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas. + + The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas. Overall design: Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients. [UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change. + GSE212527 + + + + + pubmed + 38429415 + + + + + + + SRS14953076 + SAMN30631349 + GSM6534014 + + SRC171 + + 9606 + Homo sapiens + + + + + bioproject + 875907 + + + + + + + source_name + Undifferentiated pleomorphic sarcoma + + + tissue + Undifferentiated pleomorphic sarcoma + + + cell type + Tumor + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14953076 + SAMN30631349 + GSM6534014 + + + + + + + SRR21389612 + GSM6534014_r1 + + + + GSM6534014_r1 + + + + + loader + fastq-load.py + + + + + + SRS14953076 + SAMN30631349 + GSM6534014 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX17394930 + GSM6534012_r1 + + GSM6534012: SRC147; Homo sapiens; RNA-Seq + + + SRP395248 + PRJNA875907 + + + + + + + SRS14953074 + GSM6534012 + + + + GSM6534012 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh tumors were minced and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) using a GentleMACS Octo Dissociator with heaters (Miltenyi Biotec) following the manufacturer's instructions. Libraries were constructed using the Chromium 3' Gene Expression Solution v3.1 (10x Genomics) per the manufacturer's instructions. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499884 + SUB12076764 + + + + Moding Lab, Radiation Oncology, Stanford University School of Medicine + +
+ 450 Serra Mall + Stanford + CA + USA +
+ + Ajay + Subramanian + + + + + + SRP395248 + PRJNA875907 + GSE212527 + + + Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas. + + The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas. Overall design: Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients. [UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change. + GSE212527 + + + + + pubmed + 38429415 + + + + + + + SRS14953074 + SAMN30631351 + GSM6534012 + + SRC147 + + 9606 + Homo sapiens + + + + + bioproject + 875907 + + + + + + + source_name + Leiomyosarcoma + + + tissue + Leiomyosarcoma + + + cell type + Tumor + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS14953074 + SAMN30631351 + GSM6534012 + + + + + + + SRR21389616 + GSM6534012_r1 + + + + GSM6534012_r1 + + + + + loader + fastq-load.py + + + + + + SRS14953074 + SAMN30631351 + GSM6534012 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21389617 + GSM6534012_r2 + + + + GSM6534012_r1 + + + + + loader + fastq-load.py + + + + + + SRS14953074 + SAMN30631351 + GSM6534012 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE212576.xml b/tests/data/GSE212576.xml new file mode 100644 index 0000000..7f155c6 --- /dev/null +++ b/tests/data/GSE212576.xml @@ -0,0 +1,3297 @@ + + + + + + + SRX17403301 + GSM6537884_r1 + + GSM6537884: Caudate putamen Sample 1 3mo [CP_Y_1]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961228 + GSM6537884 + + + + GSM6537884 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + Caudate putamen Sample 1 3mo [CP_Y_1] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Caudate putamen + + + Sex + pooled male and female + + + tissue + Caudate putamen + + + strain + C57BL/6JN + + + age + 3 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + + + + + + SRR21398049 + GSM6537884_r4 + + + + GSM6537884_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L004_R1_001.fastq.gz --read2PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L004_R2_001.fastq.gz --read3PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L004_I1_001.fastq.gz + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398063 + GSM6537884_r1 + + + + GSM6537884_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L001_R1_001.fastq.gz --read2PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L001_R2_001.fastq.gz --read3PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L001_I1_001.fastq.gz + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398064 + GSM6537884_r2 + + + + GSM6537884_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L002_R1_001.fastq.gz --read2PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L002_R2_001.fastq.gz --read3PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L002_I1_001.fastq.gz + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398065 + GSM6537884_r3 + + + + GSM6537884_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L003_R1_001.fastq.gz --read2PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L003_R2_001.fastq.gz --read3PairFiles=CP_Y_1_CKDL220010337-1a-SI_GA_G4_HN2VJDSX3_S2_L003_I1_001.fastq.gz + + + + + + SRS14961228 + SAMN30644044 + GSM6537884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403300 + GSM6537887_r1 + + GSM6537887: Caudate putamen Sample 2 21mo [CP_O_2]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961227 + GSM6537887 + + + + GSM6537887 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + Caudate putamen Sample 2 21mo [CP_O_2] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Caudate putamen + + + Sex + pooled male and female + + + tissue + Caudate putamen + + + strain + C57BL/6JN + + + age + 21 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + + + + + + SRR21398050 + GSM6537887_r1 + + + + GSM6537887_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L001_R1_001.fastq.gz --read2PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L001_R2_001.fastq.gz --read3PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L001_I1_001.fastq.gz + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398051 + GSM6537887_r2 + + + + GSM6537887_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L002_R1_001.fastq.gz --read2PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L002_R2_001.fastq.gz --read3PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L002_I1_001.fastq.gz + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398052 + GSM6537887_r3 + + + + GSM6537887_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L003_R1_001.fastq.gz --read2PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L003_R2_001.fastq.gz --read3PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L003_I1_001.fastq.gz + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398053 + GSM6537887_r4 + + + + GSM6537887_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L004_R1_001.fastq.gz --read2PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L004_R2_001.fastq.gz --read3PairFiles=CP_O_2_CKDL220010340-1a-SI_GA_G7_HN2VJDSX3_S4_L004_I1_001.fastq.gz + + + + + + SRS14961227 + SAMN30644041 + GSM6537887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403299 + GSM6537886_r1 + + GSM6537886: Caudate putamen Sample 1 21mo [CP_O_1]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961226 + GSM6537886 + + + + GSM6537886 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + Caudate putamen Sample 1 21mo [CP_O_1] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Caudate putamen + + + Sex + pooled male and female + + + tissue + Caudate putamen + + + strain + C57BL/6JN + + + age + 21 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + + + + + + SRR21398054 + GSM6537886_r1 + + + + GSM6537886_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L001_R1_001.fastq.gz --read2PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L001_R2_001.fastq.gz --read3PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L001_I1_001.fastq.gz + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398055 + GSM6537886_r2 + + + + GSM6537886_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L002_R1_001.fastq.gz --read2PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L002_R2_001.fastq.gz --read3PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L002_I1_001.fastq.gz + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398056 + GSM6537886_r3 + + + + GSM6537886_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L003_R1_001.fastq.gz --read2PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L003_R2_001.fastq.gz --read3PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L003_I1_001.fastq.gz + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398057 + GSM6537886_r4 + + + + GSM6537886_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L004_R1_001.fastq.gz --read2PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L004_R2_001.fastq.gz --read3PairFiles=CP_O_1_CKDL220010339-1a-SI_GA_G6_HN2VJDSX3_S11_L004_I1_001.fastq.gz + + + + + + SRS14961226 + SAMN30644042 + GSM6537886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403298 + GSM6537885_r1 + + GSM6537885: Caudate putamen Sample 2 3mo [CP_Y_2]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961225 + GSM6537885 + + + + GSM6537885 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + Caudate putamen Sample 2 3mo [CP_Y_2] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Caudate putamen + + + Sex + pooled male and female + + + tissue + Caudate putamen + + + strain + C57BL/6JN + + + age + 3 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + + + + + + SRR21398058 + GSM6537885_r1 + + + + GSM6537885_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L001_R1_001.fastq.gz --read2PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L001_R2_001.fastq.gz --read3PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L001_I1_001.fastq.gz + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398059 + GSM6537885_r2 + + + + GSM6537885_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L002_R1_001.fastq.gz --read2PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L002_R2_001.fastq.gz --read3PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L002_I1_001.fastq.gz + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398060 + GSM6537885_r3 + + + + GSM6537885_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L003_R1_001.fastq.gz --read2PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L003_R2_001.fastq.gz --read3PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L003_I1_001.fastq.gz + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398061 + GSM6537885_r4 + + + + GSM6537885_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L004_R1_001.fastq.gz --read2PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L004_R2_001.fastq.gz --read3PairFiles=CP_Y_2_CKDL220010338-1a-SI_GA_G5_HN2VJDSX3_S3_L004_I1_001.fastq.gz + + + + + + SRS14961225 + SAMN30644043 + GSM6537885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403297 + GSM6537883_r1 + + GSM6537883: Hippocampus Sample 2 21mo [HIP_O_2]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961224 + GSM6537883 + + + + GSM6537883 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + Hippocampus Sample 2 21mo [HIP_O_2] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Hippocampus (anterior) + + + Sex + pooled male and female + + + tissue + Hippocampus (anterior) + + + strain + C57BL/6JN + + + age + 21 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + + + + + + SRR21398062 + GSM6537883_r4 + + + + GSM6537883_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L004_R1_001.fastq.gz --read2PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L004_R2_001.fastq.gz --read3PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L004_I1_001.fastq.gz + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398067 + GSM6537883_r1 + + + + GSM6537883_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L001_R1_001.fastq.gz --read2PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L001_R2_001.fastq.gz --read3PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L001_I1_001.fastq.gz + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398068 + GSM6537883_r2 + + + + GSM6537883_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L002_R1_001.fastq.gz --read2PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L002_R2_001.fastq.gz --read3PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L002_I1_001.fastq.gz + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398069 + GSM6537883_r3 + + + + GSM6537883_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L003_R1_001.fastq.gz --read2PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L003_R2_001.fastq.gz --read3PairFiles=HIP_O_2_CKDL220010346-1a-SI_GA_F9_HN2VJDSX3_S9_L003_I1_001.fastq.gz + + + + + + SRS14961224 + SAMN30644045 + GSM6537883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403296 + GSM6537882_r1 + + GSM6537882: Hippocampus Sample 1 21mo [HIP_O_1]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961223 + GSM6537882 + + + + GSM6537882 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + Hippocampus Sample 1 21mo [HIP_O_1] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Hippocampus (anterior) + + + Sex + pooled male and female + + + tissue + Hippocampus (anterior) + + + strain + C57BL/6JN + + + age + 21 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + + + + + + SRR21398066 + GSM6537882_r4 + + + + GSM6537882_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L004_R1_001.fastq.gz --read2PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L004_R2_001.fastq.gz --read3PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L004_I1_001.fastq.gz + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398071 + GSM6537882_r1 + + + + GSM6537882_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L001_R1_001.fastq.gz --read2PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L001_R2_001.fastq.gz --read3PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L001_I1_001.fastq.gz + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398072 + GSM6537882_r2 + + + + GSM6537882_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L002_R1_001.fastq.gz --read2PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L002_R2_001.fastq.gz --read3PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L002_I1_001.fastq.gz + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398073 + GSM6537882_r3 + + + + GSM6537882_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L003_R1_001.fastq.gz --read2PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L003_R2_001.fastq.gz --read3PairFiles=HIP_O_1_CKDL220010345-1a-SI_GA_F8_HN2VJDSX3_S10_L003_I1_001.fastq.gz + + + + + + SRS14961223 + SAMN30644046 + GSM6537882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403295 + GSM6537881_r1 + + GSM6537881: Hippocampus Sample 2 3mo [HIP_Y_2]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961222 + GSM6537881 + + + + GSM6537881 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + Hippocampus Sample 2 3mo [HIP_Y_2] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Hippocampus (anterior) + + + Sex + pooled male and female + + + tissue + Hippocampus (anterior) + + + strain + C57BL/6JN + + + age + 3 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + + + + + + SRR21398070 + GSM6537881_r4 + + + + GSM6537881_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L004_R1_001.fastq.gz --read2PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L004_R2_001.fastq.gz --read3PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L004_I1_001.fastq.gz + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398075 + GSM6537881_r1 + + + + GSM6537881_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L001_R1_001.fastq.gz --read2PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L001_R2_001.fastq.gz --read3PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L001_I1_001.fastq.gz + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398076 + GSM6537881_r2 + + + + GSM6537881_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L002_R1_001.fastq.gz --read2PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L002_R2_001.fastq.gz --read3PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L002_I1_001.fastq.gz + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21398077 + GSM6537881_r3 + + + + GSM6537881_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L003_R1_001.fastq.gz --read2PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L003_R2_001.fastq.gz --read3PairFiles=HIP_Y_2_CKDL220010344-1a-SI_GA_F10_HN2VJDSX3_S7_L003_I1_001.fastq.gz + + + + + + SRS14961222 + SAMN30644047 + GSM6537881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17403294 + GSM6537880_r1 + + GSM6537880: Hippocampus Sample 1 3mo [HIP_Y_1]; Mus musculus; RNA-Seq + + + SRP395351 + PRJNA876097 + + + + + + + SRS14961221 + GSM6537880 + + + + GSM6537880 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from left hemisphere brain region punches were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 25k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). At this stage, samples were multiplexed during sorting by combining an equal number of nuclei from 1 male and 1 female sample of the same age group. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.1 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1502799 + SUB12087594 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP395351 + PRJNA876097 + GSE212576 + + + Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age + + Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice. Overall design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1). + GSE212576 + + + + + pubmed + 37591239 + + + + + + + SRS14961221 + SAMN30644048 + GSM6537880 + + Hippocampus Sample 1 3mo [HIP_Y_1] + + 10090 + Mus musculus + + + + + bioproject + 876097 + + + + + + + source_name + Hippocampus (anterior) + + + Sex + pooled male and female + + + tissue + Hippocampus (anterior) + + + strain + C57BL/6JN + + + age + 3 months + + + molecule subtype + single-nuclei RNA + + + + + + + SRS14961221 + SAMN30644048 + GSM6537880 + + + + + + + SRR21398074 + GSM6537880_r1 + + + + GSM6537880_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=HIP_Y_1_R1.fq.gz --read2PairFiles=HIP_Y_1_R2.fq.gz --read3PairFiles=HIP_Y_1_I1.fq.gz + + + + + + SRS14961221 + SAMN30644048 + GSM6537880 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + diff --git a/tests/data/GSE213364.xml b/tests/data/GSE213364.xml new file mode 100644 index 0000000..d454e0e --- /dev/null +++ b/tests/data/GSE213364.xml @@ -0,0 +1,1512 @@ + + + + + + + SRX17577178 + GSM6581153_r1 + + GSM6581153: JLE33; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116895 + GSM6581153 + + + + GSM6581153 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116895 + SAMN30854433 + GSM6581153 + + JLE33 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + seizure-affected brain tissue + + + diagnosis + Focal cortical dysplasia type I + + + + + + + SRS15116895 + SAMN30854433 + GSM6581153 + + + + + + + SRR21575007 + GSM6581153_r1 + + + + GSM6581153_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=JLE-33_S2_L001_R1_001.fastq.gz --read2PairFiles=JLE-33_S2_L001_R2_001.fastq.gz --read3PairFiles=JLE-33_S2_L001_I1_001.fastq.gz + + + + + + SRS15116895 + SAMN30854433 + GSM6581153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21575008 + GSM6581153_r2 + + + + GSM6581153_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=JLE-33_S2_L002_R1_001.fastq.gz --read2PairFiles=JLE-33_S2_L002_R2_001.fastq.gz --read3PairFiles=JLE-33_S2_L002_I1_001.fastq.gz + + + + + + SRS15116895 + SAMN30854433 + GSM6581153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17577177 + GSM6581152_r1 + + GSM6581152: JLE18; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116894 + GSM6581152 + + + + GSM6581152 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116894 + SAMN30854434 + GSM6581152 + + JLE18 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + seizure-affected brain tissue + + + diagnosis + Focal cortical dysplasia type I + + + + + + + SRS15116894 + SAMN30854434 + GSM6581152 + + + + + + + SRR21575009 + GSM6581152_r1 + + + + GSM6581152_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=JLE-18_S1_L001_R1_001.fastq.gz --read2PairFiles=JLE-18_S1_L001_R2_001.fastq.gz --read3PairFiles=JLE-18_S1_L001_I1_001.fastq.gz + + + + + + SRS15116894 + SAMN30854434 + GSM6581152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21575010 + GSM6581152_r2 + + + + GSM6581152_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=JLE-18_S1_L002_R1_001.fastq.gz --read2PairFiles=JLE-18_S1_L002_R2_001.fastq.gz --read3PairFiles=JLE-18_S1_L002_I1_001.fastq.gz + + + + + + SRS15116894 + SAMN30854434 + GSM6581152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17577176 + GSM6581151_r1 + + GSM6581151: NB4327; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116893 + GSM6581151 + + + + GSM6581151 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116893 + SAMN30854435 + GSM6581151 + + NB4327 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + autopsy control brain tissue + + + diagnosis + none + + + + + + + SRS15116893 + SAMN30854435 + GSM6581151 + + + + + + + SRR21575011 + GSM6581151_r1 + + + + GSM6581151_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=NB4327_10x_S5_L001_R1_001.fastq.gz --read2PairFiles=NB4327_10x_S5_L001_R2_001.fastq.gz --read3PairFiles=NB4327_10x_S5_L001_I1_001.fastq.gz + + + + + + SRS15116893 + SAMN30854435 + GSM6581151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17577175 + GSM6581150_r1 + + GSM6581150: NB1499; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116892 + GSM6581150 + + + + GSM6581150 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116892 + SAMN30854436 + GSM6581150 + + NB1499 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + autopsy control brain tissue + + + diagnosis + none + + + + + + + SRS15116892 + SAMN30854436 + GSM6581150 + + + + + + + SRR21575012 + GSM6581150_r1 + + + + GSM6581150_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=NB1499_10x_S4_L001_R1_001.fastq.gz --read2PairFiles=NB1499_10x_S4_L001_R2_001.fastq.gz --read3PairFiles=NB1499_10x_S4_L001_I1_001.fastq.gz + + + + + + SRS15116892 + SAMN30854436 + GSM6581150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17577174 + GSM6581149_r1 + + GSM6581149: JLE23; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116891 + GSM6581149 + + + + GSM6581149 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116891 + SAMN30854437 + GSM6581149 + + JLE23 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + seizure-affected brain tissue + + + diagnosis + Rasmussen Encephalitis + + + + + + + SRS15116891 + SAMN30854437 + GSM6581149 + + + + + + + SRR21575013 + GSM6581149_r1 + + + + GSM6581149_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L001_R1_001.fastq.gz --read2PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L001_R2_001.fastq.gz --read3PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L001_I1_001.fastq.gz + + + + + + SRS15116891 + SAMN30854437 + GSM6581149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21575014 + GSM6581149_r2 + + + + GSM6581149_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L002_R1_001.fastq.gz --read2PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L002_R2_001.fastq.gz --read3PairFiles=Y6377_WilsonR_23_V1G_1a_S3_L002_I1_001.fastq.gz + + + + + + SRS15116891 + SAMN30854437 + GSM6581149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17577173 + GSM6581148_r1 + + GSM6581148: JLE20; Homo sapiens; RNA-Seq + + + SRP397145 + PRJNA880601 + + + + + + + SRS15116890 + GSM6581148 + + + + GSM6581148 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3' reagent kits. 10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol. paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1499044 + SUB12068532 + + + + Institute for Genomic Medicine, Nationwide Children's Hospital + +
+ 700 Children’s Drive + Columbus + OH + USA +
+ + Alessandro + Canella + + + + + + SRP397145 + PRJNA880601 + GSE213364 + + + Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis + + Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated upregulation of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE. Overall design: We performed a comparitive analysis of single cell gene expression (10X Genomics 3' v3.1) between cortical tissue from patients with Rasmussen Encephalitis and from both non-diseased controls and a non-inflammatory epilepsy (Focal cortical dysplasia type I) samples. After QC and normalization, single cell gene expression datasets were integrated and cell types were determined using a combination of canonical markers and reference from Allen Barin Map [6] (Figure 1). We perfomed diffferential expression (DE) analysis via DESeq2 [28] and Gene Ontology (GO) Anotation enrichment analysis [13] of microglia across disease contitions (Figure 2). Louvain clustering was performed on the microglia and subsequent DE and GO annotation enrichment analysis were perfomed between the clusters (Figure 3). + GSE213364 + + + + + pubmed + 36411471 + + + + + + + SRS15116890 + SAMN30854438 + GSM6581148 + + JLE20 + + 9606 + Homo sapiens + + + + + bioproject + 880601 + + + + + + + source_name + seizure-affected brain tissue + + + diagnosis + Rasmussen Encephalitis + + + + + + + SRS15116890 + SAMN30854438 + GSM6581148 + + + + + + + SRR21575015 + GSM6581148_r1 + + + + GSM6581148_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L001_R1_001.fastq.gz --read2PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L001_R2_001.fastq.gz --read3PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L001_I1_001.fastq.gz + + + + + + SRS15116890 + SAMN30854438 + GSM6581148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21575016 + GSM6581148_r2 + + + + GSM6581148_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBT --read1PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L002_R1_001.fastq.gz --read2PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L002_R2_001.fastq.gz --read3PairFiles=Y6376_WilsonR_20_V1G_1a_S2_L002_I1_001.fastq.gz + + + + + + SRS15116890 + SAMN30854438 + GSM6581148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE214244.xml b/tests/data/GSE214244.xml new file mode 100644 index 0000000..85c7558 --- /dev/null +++ b/tests/data/GSE214244.xml @@ -0,0 +1,2940 @@ + + + + + + + SRX17717814 + GSM6602015_r1 + + GSM6602015: EC.WT.2; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247905 + GSM6602015 + + + + GSM6602015 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + EC.WT.2 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Entorhinal cortex + + + tissue + Entorhinal cortex + + + strain + C57BL6J + + + Sex + male + + + genotype + Wild-type + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + + + + + + SRR21720716 + GSM6602015_r1 + + + + GSM6602015_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720725 + GSM6602015_r2 + + + + GSM6602015_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720726 + GSM6602015_r3 + + + + GSM6602015_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720727 + GSM6602015_r4 + + + + GSM6602015_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247905 + SAMN31028766 + GSM6602015 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717813 + GSM6602016_r1 + + GSM6602016: EC.APP.2; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247904 + GSM6602016 + + + + GSM6602016 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247904 + SAMN31028765 + GSM6602016 + + EC.APP.2 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Entorhinal cortex + + + tissue + Entorhinal cortex + + + strain + C57BL6J + + + Sex + male + + + genotype + AppNL-G-F/NL-G-F + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247904 + SAMN31028765 + GSM6602016 + + + + + + + SRR21720717 + GSM6602016_r1 + + + + GSM6602016_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247904 + SAMN31028765 + GSM6602016 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR21720720 + GSM6602016_r4 + + + + GSM6602016_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247904 + SAMN31028765 + GSM6602016 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717812 + GSM6602014_r1 + + GSM6602014: DCN.APP.2; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247903 + GSM6602014 + + + + GSM6602014 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247903 + SAMN31028767 + GSM6602014 + + DCN.APP.2 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Deep cerebellar nuclei + + + tissue + Deep cerebellar nuclei + + + strain + C57BL6J + + + Sex + male + + + genotype + AppNL-G-F/NL-G-F + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247903 + SAMN31028767 + GSM6602014 + + + + + + + SRR21720721 + GSM6602014_r1 + + + + GSM6602014_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247903 + SAMN31028767 + GSM6602014 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR21720724 + GSM6602014_r4 + + + + GSM6602014_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247903 + SAMN31028767 + GSM6602014 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717811 + GSM6602013_r1 + + GSM6602013: DCN.WT.2; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247902 + GSM6602013 + + + + GSM6602013 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247902 + SAMN31028768 + GSM6602013 + + DCN.WT.2 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Deep cerebellar nuclei + + + tissue + Deep cerebellar nuclei + + + strain + C57BL6J + + + Sex + male + + + genotype + Wild-type + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247902 + SAMN31028768 + GSM6602013 + + + + + + + SRR21720728 + GSM6602013_r1 + + + + GSM6602013_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247902 + SAMN31028768 + GSM6602013 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX17717810 + GSM6602012_r1 + + GSM6602012: EC.APP.1; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247901 + GSM6602012 + + + + GSM6602012 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247901 + SAMN31028769 + GSM6602012 + + EC.APP.1 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Entorhinal cortex + + + tissue + Entorhinal cortex + + + strain + C57BL6J + + + Sex + male + + + genotype + AppNL-G-F/NL-G-F + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247901 + SAMN31028769 + GSM6602012 + + + + + + + SRR21720729 + GSM6602012_r1 + + + + GSM6602012_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247901 + SAMN31028769 + GSM6602012 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720736 + GSM6602012_r2 + + + + GSM6602012_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247901 + SAMN31028769 + GSM6602012 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717809 + GSM6602011_r1 + + GSM6602011: EC.WT.1; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247900 + GSM6602011 + + + + GSM6602011 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247900 + SAMN31028770 + GSM6602011 + + EC.WT.1 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Entorhinal cortex + + + tissue + Entorhinal cortex + + + strain + C57BL6J + + + Sex + male + + + genotype + Wild-type + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247900 + SAMN31028770 + GSM6602011 + + + + + + + SRR21720730 + GSM6602011_r1 + + + + GSM6602011_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247900 + SAMN31028770 + GSM6602011 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720735 + GSM6602011_r2 + + + + GSM6602011_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247900 + SAMN31028770 + GSM6602011 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717808 + GSM6602009_r1 + + GSM6602009: DCN.WT.1; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247898 + GSM6602009 + + + + GSM6602009 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247898 + SAMN31028772 + GSM6602009 + + DCN.WT.1 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Deep cerebellar nuclei + + + tissue + Deep cerebellar nuclei + + + strain + C57BL6J + + + Sex + male + + + genotype + Wild-type + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247898 + SAMN31028772 + GSM6602009 + + + + + + + SRR21720731 + GSM6602009_r1 + + + + GSM6602009_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247898 + SAMN31028772 + GSM6602009 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720732 + GSM6602009_r2 + + + + GSM6602009_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247898 + SAMN31028772 + GSM6602009 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX17717807 + GSM6602010_r1 + + GSM6602010: DCN.APP.1; Mus musculus; RNA-Seq + + + SRP399763 + PRJNA884479 + + + + + + + SRS15247899 + GSM6602010 + + + + GSM6602010 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anaesthetized with isoflurane before decapitation. Brains were dissected on ice and rested in pre-bubbled slurry cutting solution [250 mM sucrose, 26 mM NaHCO3, 10 mM [D+] glucose, 3 mM myo-inositol, 2.5 mM KCl, 2 mM sodium pyruvate, 1.25 mM NaH2PO4·2H2O, 0.5 mM ascorbic acid, 1 mM kynurenic acid, 0.1 mM CaCl2 and 4 mM MgCl2] for 1 min. A downward cut across the midbrain was made to separate the cerebellum from the frontal cortex. To dissect DCN, the cerebellum was first sectioned at 300µm in cold cutting solution using a vibratome [Leica VT-1200]. Approximately 4-5 sections were used to microdissect the DCN in chilled pre-bubbled artificial cerebrospinal fluid [ACSF: 10 mM [D+] glucose, 126 mM NaCl, 24 mM NaHCO3, 1 mM NaH2PO4·2H2O, 2.5mM KCl, 0.4mM ascorbic acid, 2 mM CaCl2 and 2 mM MgCl2] under a light microscope. For EC dissection, a longitudinal cut was made to separate the two hemispheres. With the medial surface of the hemispheres facing up, the thalamic and hypothalamic region were scooped outpeeled back and removed, exposing the hippocampal formation. The hippocampus region was further rolled out, with the hippocampus remaining attached to the EC via the subiculum. The entorhinal cortex was then dissected by making four cuts: one vertical cut was made parallel to the join between the hpc and EC, roughly one hippocampus width away; then horizontal cuts were made at the top and bottom of the join, and finally a vertical cut was made to sever the EC and hippocampus. Dissected tissues were transferred to chilled homogenisation buffer [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8] in a Dounce homogeniser and homogenised with 10 strokes of the pestle. To lyse the samples, NP-40 detergent was added to obtain a final concentration of 0.3% and samples were dounced with 5 additional strokes. Lysates were filtered using 40um FlowMi tip strainers to remove debris and clumped nuclei. Each 2ml sample was gently mixed with 4.6ml 1.8M sucrose cushion buffer [1.8M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9] and layered over a 3ml sucrose cushion. Samples were spun in an ultracentrifuge at 30,000 x g for 45 mins at 4°C. The supernatant was then removed and pellets were resuspended in 90ul nuclei resuspension buffer [10mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, 1.5 mM CaCl2, pH 6.9]. Nuclei were inspected and counted under a microscope using a hemocytometer and Trypan blue dye. cDNA libraries were generated according to manufacturer's protocol (10x Genomics, Inc.). In brief, approximately 10, 000 nuclei per sample were processed using the Chromiium Single Cell 3' v3 Gene Expression kit. The libraries were subsequently sequenced using NovaSeq6000 (NovogeneAIT Genomics). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1508418 + SUB12104895 + + + + Ch'ng TH, LKC Medicine, Nanyang Technological University + +
+ 11 Mandalay Road + Singapore + Singapore +
+ + Jessica + Gaunt + + + + + + SRP399763 + PRJNA884479 + GSE214244 + + + Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer's disease + + Alzheimer's Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aß plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months. Overall design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method. + GSE214244 + + + + + pubmed + 37978387 + + + + + + parent_bioproject + PRJNA924794 + + + + + + SRS15247899 + SAMN31028771 + GSM6602010 + + DCN.APP.1 + + 10090 + Mus musculus + + + + + bioproject + 884479 + + + + + + + source_name + Deep cerebellar nuclei + + + tissue + Deep cerebellar nuclei + + + strain + C57BL6J + + + Sex + male + + + genotype + AppNL-G-F/NL-G-F + + + age + 7 months + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15247899 + SAMN31028771 + GSM6602010 + + + + + + + SRR21720733 + GSM6602010_r1 + + + + GSM6602010_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247899 + SAMN31028771 + GSM6602010 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR21720734 + GSM6602010_r2 + + + + GSM6602010_r1 + + + + + loader + fastq-load.py + + + + + + SRS15247899 + SAMN31028771 + GSM6602010 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE216766.xml b/tests/data/GSE216766.xml new file mode 100644 index 0000000..24a28e7 --- /dev/null +++ b/tests/data/GSE216766.xml @@ -0,0 +1,1548 @@ + + + + + + + SRX18057932 + GSM6690591_r1 + + GSM6690591: CrT-KO (Replicate 2); Mus musculus; RNA-Seq + + + SRP405045 + PRJNA895358 + + + + + + + SRS15563769 + GSM6690591 + + + + GSM6690591 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were acutely purified from brain cortex as described previously with minor modifications (Cid et al., 2021). Brains were immediately removed into ice cold HBBS 1x. A total of four libraries were generated; two libraries per condition (CrT+/y and CrT-/y) were prepared, corresponding to independent biological replicates. For each library, the cerebral cortex of the right hemisphere was manually dissected and transferred into 1 mL of ice-cold MACS buffer (0,5% BSA, 2 mM EDTA, PBS 1x). Each cortex was then homogeneized 12-15 times with the pestle of a dounce homogeneizer (20404, Lab Unlimited, Dublin, Ireland). Cell suspensions were passed through a 40 m cell strainer, collected in a 2 mL tube and centrifuged for 15 min (500G, 4ºC). The resulting cell pellets were resuspended in 1 mL of lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and transferred into a 15 mL falcon tube containing 9 mL of cell lysis buffer. The cell suspension was kept 5 min on ice, inverting the tube to mix the suspension every 1 minute. Samples were then spun down at 500G for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA, RNase inhibitor 0,2 U/L (3335399001, Merck, Darmstadt, Germany) and 15000 nuclei were purified by flow cytometry in a BD FACS Aria III (BD Biosciences, Madrid, Spain). The whole process was carried out at 4ºC. Purified intact nuclei were processed through all steps to generate stable cDNA libraries. For every sample, 15000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics, Pleasanton, USA) and processed following the manufacturer's instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads following manufacturer instructions. Libraries were sequenced to obtain more than 900 million reads in total (WT_1:>240M; WT_2:>238M; KO_1:>300M; KO_2:>209M). snRNA-seq + + + + + Illumina HiSeq 2500 + + + + + + SRA1529443 + SUB12225305 + + + + Instituto de Neurociencias + +
+ Av. Santiago Ramón y Cajal, s/n + San Juan de Alicante + Spain +
+ + Ángel + Márquez Galera + + + + + + SRP405045 + PRJNA895358 + GSE216766 + + + Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency + + Mutations in the solute carrier family 6-member 8 (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with intellectual disability, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood, hindering the development of therapies. In this study, we generated an extensive transcriptomic profile of CTD showing that Cr deficiency causes perturbations of gene expression in excitatory neurons, inhibitory cells, and oligodendrocytes which result in remodeling of circuit excitability and synaptic wiring. We also identified specific alterations of parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional electrophysiological phenotype. Mice lacking Slc6a8 only in PV+ interneurons recapitulated numerous CTD features, including cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ interneurons is sufficient to determine the neurological phenotype of CTD. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses significantly improved cortical activity in Slc6a8 knock-out animals. Altogether, these data demonstrate that Slc6a8 is critical for the normal function of PV+ interneurons and that impairment of these cells is central in the disease pathogenesis, suggesting a novel therapeutic venue for CTD. Overall design: snRNA-seq analysis of control and CrT-KO cells from the cerebral cortex. + GSE216766 + + + + + pubmed + 36882863 + + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + CrT-KO (Replicate 2) + + 10090 + Mus musculus + + + + + bioproject + 895358 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Cortex cells + + + genotype + CrT-/y + + + treatment + No treatment + + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + + + + + + SRR22077690 + GSM6690591_r1 + + + + GSM6690591_r1 + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077691 + GSM6690591_r2 + + + + GSM6690591_r1 + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077692 + GSM6690591_r3 + + + + GSM6690591_r1 + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077693 + GSM6690591_r4 + + + + GSM6690591_r1 + + + + + + SRS15563769 + SAMN31501531 + GSM6690591 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18057931 + GSM6690590_r1 + + GSM6690590: CrT-KO (Replicate 1); Mus musculus; RNA-Seq + + + SRP405045 + PRJNA895358 + + + + + + + SRS15563768 + GSM6690590 + + + + GSM6690590 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were acutely purified from brain cortex as described previously with minor modifications (Cid et al., 2021). Brains were immediately removed into ice cold HBBS 1x. A total of four libraries were generated; two libraries per condition (CrT+/y and CrT-/y) were prepared, corresponding to independent biological replicates. For each library, the cerebral cortex of the right hemisphere was manually dissected and transferred into 1 mL of ice-cold MACS buffer (0,5% BSA, 2 mM EDTA, PBS 1x). Each cortex was then homogeneized 12-15 times with the pestle of a dounce homogeneizer (20404, Lab Unlimited, Dublin, Ireland). Cell suspensions were passed through a 40 m cell strainer, collected in a 2 mL tube and centrifuged for 15 min (500G, 4ºC). The resulting cell pellets were resuspended in 1 mL of lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and transferred into a 15 mL falcon tube containing 9 mL of cell lysis buffer. The cell suspension was kept 5 min on ice, inverting the tube to mix the suspension every 1 minute. Samples were then spun down at 500G for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA, RNase inhibitor 0,2 U/L (3335399001, Merck, Darmstadt, Germany) and 15000 nuclei were purified by flow cytometry in a BD FACS Aria III (BD Biosciences, Madrid, Spain). The whole process was carried out at 4ºC. Purified intact nuclei were processed through all steps to generate stable cDNA libraries. For every sample, 15000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics, Pleasanton, USA) and processed following the manufacturer's instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads following manufacturer instructions. Libraries were sequenced to obtain more than 900 million reads in total (WT_1:>240M; WT_2:>238M; KO_1:>300M; KO_2:>209M). snRNA-seq + + + + + Illumina HiSeq 2500 + + + + + + SRA1529443 + SUB12225305 + + + + Instituto de Neurociencias + +
+ Av. Santiago Ramón y Cajal, s/n + San Juan de Alicante + Spain +
+ + Ángel + Márquez Galera + + + + + + SRP405045 + PRJNA895358 + GSE216766 + + + Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency + + Mutations in the solute carrier family 6-member 8 (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with intellectual disability, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood, hindering the development of therapies. In this study, we generated an extensive transcriptomic profile of CTD showing that Cr deficiency causes perturbations of gene expression in excitatory neurons, inhibitory cells, and oligodendrocytes which result in remodeling of circuit excitability and synaptic wiring. We also identified specific alterations of parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional electrophysiological phenotype. Mice lacking Slc6a8 only in PV+ interneurons recapitulated numerous CTD features, including cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ interneurons is sufficient to determine the neurological phenotype of CTD. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses significantly improved cortical activity in Slc6a8 knock-out animals. Altogether, these data demonstrate that Slc6a8 is critical for the normal function of PV+ interneurons and that impairment of these cells is central in the disease pathogenesis, suggesting a novel therapeutic venue for CTD. Overall design: snRNA-seq analysis of control and CrT-KO cells from the cerebral cortex. + GSE216766 + + + + + pubmed + 36882863 + + + + + + + SRS15563768 + SAMN31501532 + GSM6690590 + + CrT-KO (Replicate 1) + + 10090 + Mus musculus + + + + + bioproject + 895358 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Cortex cells + + + genotype + CrT-/y + + + treatment + No treatment + + + + + + + SRS15563768 + SAMN31501532 + GSM6690590 + + + + + + + SRR22077694 + GSM6690590_r1 + + + + GSM6690590_r1 + + + + + + SRS15563768 + SAMN31501532 + GSM6690590 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR22077696 + GSM6690590_r3 + + + + GSM6690590_r1 + + + + + + SRS15563768 + SAMN31501532 + GSM6690590 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077697 + GSM6690590_r4 + + + + GSM6690590_r1 + + + + + + SRS15563768 + SAMN31501532 + GSM6690590 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18057930 + GSM6690589_r1 + + GSM6690589: Control (Replicate 2); Mus musculus; RNA-Seq + + + SRP405045 + PRJNA895358 + + + + + + + SRS15563767 + GSM6690589 + + + + GSM6690589 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were acutely purified from brain cortex as described previously with minor modifications (Cid et al., 2021). Brains were immediately removed into ice cold HBBS 1x. A total of four libraries were generated; two libraries per condition (CrT+/y and CrT-/y) were prepared, corresponding to independent biological replicates. For each library, the cerebral cortex of the right hemisphere was manually dissected and transferred into 1 mL of ice-cold MACS buffer (0,5% BSA, 2 mM EDTA, PBS 1x). Each cortex was then homogeneized 12-15 times with the pestle of a dounce homogeneizer (20404, Lab Unlimited, Dublin, Ireland). Cell suspensions were passed through a 40 m cell strainer, collected in a 2 mL tube and centrifuged for 15 min (500G, 4ºC). The resulting cell pellets were resuspended in 1 mL of lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and transferred into a 15 mL falcon tube containing 9 mL of cell lysis buffer. The cell suspension was kept 5 min on ice, inverting the tube to mix the suspension every 1 minute. Samples were then spun down at 500G for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA, RNase inhibitor 0,2 U/L (3335399001, Merck, Darmstadt, Germany) and 15000 nuclei were purified by flow cytometry in a BD FACS Aria III (BD Biosciences, Madrid, Spain). The whole process was carried out at 4ºC. Purified intact nuclei were processed through all steps to generate stable cDNA libraries. For every sample, 15000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics, Pleasanton, USA) and processed following the manufacturer's instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads following manufacturer instructions. Libraries were sequenced to obtain more than 900 million reads in total (WT_1:>240M; WT_2:>238M; KO_1:>300M; KO_2:>209M). snRNA-seq + + + + + Illumina HiSeq 2500 + + + + + + SRA1529443 + SUB12225305 + + + + Instituto de Neurociencias + +
+ Av. Santiago Ramón y Cajal, s/n + San Juan de Alicante + Spain +
+ + Ángel + Márquez Galera + + + + + + SRP405045 + PRJNA895358 + GSE216766 + + + Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency + + Mutations in the solute carrier family 6-member 8 (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with intellectual disability, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood, hindering the development of therapies. In this study, we generated an extensive transcriptomic profile of CTD showing that Cr deficiency causes perturbations of gene expression in excitatory neurons, inhibitory cells, and oligodendrocytes which result in remodeling of circuit excitability and synaptic wiring. We also identified specific alterations of parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional electrophysiological phenotype. Mice lacking Slc6a8 only in PV+ interneurons recapitulated numerous CTD features, including cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ interneurons is sufficient to determine the neurological phenotype of CTD. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses significantly improved cortical activity in Slc6a8 knock-out animals. Altogether, these data demonstrate that Slc6a8 is critical for the normal function of PV+ interneurons and that impairment of these cells is central in the disease pathogenesis, suggesting a novel therapeutic venue for CTD. Overall design: snRNA-seq analysis of control and CrT-KO cells from the cerebral cortex. + GSE216766 + + + + + pubmed + 36882863 + + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + Control (Replicate 2) + + 10090 + Mus musculus + + + + + bioproject + 895358 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Cortex cells + + + genotype + Control + + + treatment + No treatment + + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + + + + + + SRR22077698 + GSM6690589_r1 + + + + GSM6690589_r1 + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077699 + GSM6690589_r2 + + + + GSM6690589_r1 + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077700 + GSM6690589_r3 + + + + GSM6690589_r1 + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077701 + GSM6690589_r4 + + + + GSM6690589_r1 + + + + + + SRS15563767 + SAMN31501533 + GSM6690589 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18057929 + GSM6690588_r1 + + GSM6690588: Control (Replicate 1); Mus musculus; RNA-Seq + + + SRP405045 + PRJNA895358 + + + + + + + SRS15563766 + GSM6690588 + + + + GSM6690588 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were acutely purified from brain cortex as described previously with minor modifications (Cid et al., 2021). Brains were immediately removed into ice cold HBBS 1x. A total of four libraries were generated; two libraries per condition (CrT+/y and CrT-/y) were prepared, corresponding to independent biological replicates. For each library, the cerebral cortex of the right hemisphere was manually dissected and transferred into 1 mL of ice-cold MACS buffer (0,5% BSA, 2 mM EDTA, PBS 1x). Each cortex was then homogeneized 12-15 times with the pestle of a dounce homogeneizer (20404, Lab Unlimited, Dublin, Ireland). Cell suspensions were passed through a 40 m cell strainer, collected in a 2 mL tube and centrifuged for 15 min (500G, 4ºC). The resulting cell pellets were resuspended in 1 mL of lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and transferred into a 15 mL falcon tube containing 9 mL of cell lysis buffer. The cell suspension was kept 5 min on ice, inverting the tube to mix the suspension every 1 minute. Samples were then spun down at 500G for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA, RNase inhibitor 0,2 U/L (3335399001, Merck, Darmstadt, Germany) and 15000 nuclei were purified by flow cytometry in a BD FACS Aria III (BD Biosciences, Madrid, Spain). The whole process was carried out at 4ºC. Purified intact nuclei were processed through all steps to generate stable cDNA libraries. For every sample, 15000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics, Pleasanton, USA) and processed following the manufacturer's instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads following manufacturer instructions. Libraries were sequenced to obtain more than 900 million reads in total (WT_1:>240M; WT_2:>238M; KO_1:>300M; KO_2:>209M). snRNA-seq + + + + + Illumina HiSeq 2500 + + + + + + SRA1529443 + SUB12225305 + + + + Instituto de Neurociencias + +
+ Av. Santiago Ramón y Cajal, s/n + San Juan de Alicante + Spain +
+ + Ángel + Márquez Galera + + + + + + SRP405045 + PRJNA895358 + GSE216766 + + + Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency + + Mutations in the solute carrier family 6-member 8 (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with intellectual disability, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood, hindering the development of therapies. In this study, we generated an extensive transcriptomic profile of CTD showing that Cr deficiency causes perturbations of gene expression in excitatory neurons, inhibitory cells, and oligodendrocytes which result in remodeling of circuit excitability and synaptic wiring. We also identified specific alterations of parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional electrophysiological phenotype. Mice lacking Slc6a8 only in PV+ interneurons recapitulated numerous CTD features, including cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ interneurons is sufficient to determine the neurological phenotype of CTD. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses significantly improved cortical activity in Slc6a8 knock-out animals. Altogether, these data demonstrate that Slc6a8 is critical for the normal function of PV+ interneurons and that impairment of these cells is central in the disease pathogenesis, suggesting a novel therapeutic venue for CTD. Overall design: snRNA-seq analysis of control and CrT-KO cells from the cerebral cortex. + GSE216766 + + + + + pubmed + 36882863 + + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + Control (Replicate 1) + + 10090 + Mus musculus + + + + + bioproject + 895358 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Cortex cells + + + genotype + Control + + + treatment + No treatment + + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + + + + + + SRR22077702 + GSM6690588_r1 + + + + GSM6690588_r1 + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077703 + GSM6690588_r2 + + + + GSM6690588_r1 + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077704 + GSM6690588_r3 + + + + GSM6690588_r1 + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22077705 + GSM6690588_r4 + + + + GSM6690588_r1 + + + + + + SRS15563766 + SAMN31501534 + GSM6690588 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE217511.xml b/tests/data/GSE217511.xml new file mode 100644 index 0000000..26b0d4c --- /dev/null +++ b/tests/data/GSE217511.xml @@ -0,0 +1,8032 @@ + + + + + + + SRX18205292 + GSM6720876_r1 + + GSM6720876: Prenatal, sample13, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702483 + GSM6720876 + + + + GSM6720876 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702483 + SAMN31656495 + GSM6720876 + + Prenatal, sample13, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 32.8 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702483 + SAMN31656495 + GSM6720876 + + + + + + + SRR22227667 + GSM6720876_r1 + + + + GSM6720876_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702483 + SAMN31656495 + GSM6720876 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205291 + GSM6720875_r1 + + GSM6720875: Prenatal, sample12, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702482 + GSM6720875 + + + + GSM6720875 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702482 + SAMN31656496 + GSM6720875 + + Prenatal, sample12, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 26 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702482 + SAMN31656496 + GSM6720875 + + + + + + + SRR22227668 + GSM6720875_r1 + + + + GSM6720875_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702482 + SAMN31656496 + GSM6720875 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205290 + GSM6720874_r1 + + GSM6720874: Prenatal, sample12, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702481 + GSM6720874 + + + + GSM6720874 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702481 + SAMN31656497 + GSM6720874 + + Prenatal, sample12, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 26 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702481 + SAMN31656497 + GSM6720874 + + + + + + + SRR22227669 + GSM6720874_r1 + + + + GSM6720874_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702481 + SAMN31656497 + GSM6720874 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205289 + GSM6720873_r1 + + GSM6720873: Prenatal, sample11, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702480 + GSM6720873 + + + + GSM6720873 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702480 + SAMN31656498 + GSM6720873 + + Prenatal, sample11, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 25.8 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702480 + SAMN31656498 + GSM6720873 + + + + + + + SRR22227670 + GSM6720873_r1 + + + + GSM6720873_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702480 + SAMN31656498 + GSM6720873 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205288 + GSM6720872_r1 + + GSM6720872: Prenatal, sample11, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702479 + GSM6720872 + + + + GSM6720872 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702479 + SAMN31656499 + GSM6720872 + + Prenatal, sample11, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 25.8 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702479 + SAMN31656499 + GSM6720872 + + + + + + + SRR22227671 + GSM6720872_r1 + + + + GSM6720872_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702479 + SAMN31656499 + GSM6720872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205287 + GSM6720871_r1 + + GSM6720871: Prenatal, sample10, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702478 + GSM6720871 + + + + GSM6720871 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702478 + SAMN31656500 + GSM6720871 + + Prenatal, sample10, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 24.7 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702478 + SAMN31656500 + GSM6720871 + + + + + + + SRR22227672 + GSM6720871_r1 + + + + GSM6720871_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702478 + SAMN31656500 + GSM6720871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205286 + GSM6720870_r1 + + GSM6720870: Prenatal, sample10, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702477 + GSM6720870 + + + + GSM6720870 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702477 + SAMN31656501 + GSM6720870 + + Prenatal, sample10, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 24.7 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702477 + SAMN31656501 + GSM6720870 + + + + + + + SRR22227673 + GSM6720870_r1 + + + + GSM6720870_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702477 + SAMN31656501 + GSM6720870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205285 + GSM6720869_r1 + + GSM6720869: Prenatal, sample9, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702476 + GSM6720869 + + + + GSM6720869 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702476 + SAMN31656502 + GSM6720869 + + Prenatal, sample9, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 23.7 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702476 + SAMN31656502 + GSM6720869 + + + + + + + SRR22227674 + GSM6720869_r1 + + + + GSM6720869_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702476 + SAMN31656502 + GSM6720869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205284 + GSM6720868_r1 + + GSM6720868: Prenatal, sample9, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702475 + GSM6720868 + + + + GSM6720868 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702475 + SAMN31656503 + GSM6720868 + + Prenatal, sample9, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 23.7 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702475 + SAMN31656503 + GSM6720868 + + + + + + + SRR22227675 + GSM6720868_r1 + + + + GSM6720868_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702475 + SAMN31656503 + GSM6720868 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205283 + GSM6720867_r1 + + GSM6720867: Prenatal, sample8, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702474 + GSM6720867 + + + + GSM6720867 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702474 + SAMN31656504 + GSM6720867 + + Prenatal, sample8, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 23.3 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702474 + SAMN31656504 + GSM6720867 + + + + + + + SRR22227676 + GSM6720867_r1 + + + + GSM6720867_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702474 + SAMN31656504 + GSM6720867 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205282 + GSM6720866_r1 + + GSM6720866: Prenatal, sample8, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702473 + GSM6720866 + + + + GSM6720866 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702473 + SAMN31656505 + GSM6720866 + + Prenatal, sample8, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 23.3 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702473 + SAMN31656505 + GSM6720866 + + + + + + + SRR22227677 + GSM6720866_r1 + + + + GSM6720866_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702473 + SAMN31656505 + GSM6720866 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205281 + GSM6720865_r1 + + GSM6720865: Prenatal, sample7, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702472 + GSM6720865 + + + + GSM6720865 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702472 + SAMN31656506 + GSM6720865 + + Prenatal, sample7, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 22 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702472 + SAMN31656506 + GSM6720865 + + + + + + + SRR22227678 + GSM6720865_r1 + + + + GSM6720865_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702472 + SAMN31656506 + GSM6720865 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205280 + GSM6720864_r1 + + GSM6720864: Prenatal, sample7, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702471 + GSM6720864 + + + + GSM6720864 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702471 + SAMN31656507 + GSM6720864 + + Prenatal, sample7, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 22 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702471 + SAMN31656507 + GSM6720864 + + + + + + + SRR22227679 + GSM6720864_r1 + + + + GSM6720864_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702471 + SAMN31656507 + GSM6720864 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205279 + GSM6720863_r1 + + GSM6720863: Prenatal, sample6, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702470 + GSM6720863 + + + + GSM6720863 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702470 + SAMN31656508 + GSM6720863 + + Prenatal, sample6, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 21.3 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702470 + SAMN31656508 + GSM6720863 + + + + + + + SRR22227680 + GSM6720863_r1 + + + + GSM6720863_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702470 + SAMN31656508 + GSM6720863 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205278 + GSM6720862_r1 + + GSM6720862: Prenatal, sample6, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702469 + GSM6720862 + + + + GSM6720862 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702469 + SAMN31656509 + GSM6720862 + + Prenatal, sample6, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 21.3 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702469 + SAMN31656509 + GSM6720862 + + + + + + + SRR22227681 + GSM6720862_r1 + + + + GSM6720862_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702469 + SAMN31656509 + GSM6720862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205277 + GSM6720861_r1 + + GSM6720861: Prenatal, sample5, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702468 + GSM6720861 + + + + GSM6720861 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702468 + SAMN31656510 + GSM6720861 + + Prenatal, sample5, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 20.3 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702468 + SAMN31656510 + GSM6720861 + + + + + + + SRR22227682 + GSM6720861_r1 + + + + GSM6720861_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702468 + SAMN31656510 + GSM6720861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205276 + GSM6720887_r1 + + GSM6720887: Adult, sample3, SVZ+caudate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702467 + GSM6720887 + + + + GSM6720887 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702467 + SAMN31656484 + GSM6720887 + + Adult, sample3, SVZ+caudate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, svz+caudate + + + tissue + Brain, svz+caudate + + + developmental stage + 53 years + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702467 + SAMN31656484 + GSM6720887 + + + + + + + SRR22227683 + GSM6720887_r1 + + + + GSM6720887_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702467 + SAMN31656484 + GSM6720887 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205275 + GSM6720886_r1 + + GSM6720886: Adult, sample3, neocortex; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702466 + GSM6720886 + + + + GSM6720886 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702466 + SAMN31656485 + GSM6720886 + + Adult, sample3, neocortex + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, neocortex + + + tissue + Brain, neocortex + + + developmental stage + 53 years + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702466 + SAMN31656485 + GSM6720886 + + + + + + + SRR22227684 + GSM6720886_r1 + + + + GSM6720886_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702466 + SAMN31656485 + GSM6720886 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205274 + GSM6720885_r1 + + GSM6720885: Adult, sample2, SVZ+caudate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702465 + GSM6720885 + + + + GSM6720885 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702465 + SAMN31656486 + GSM6720885 + + Adult, sample2, SVZ+caudate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, svz+caudate + + + tissue + Brain, svz+caudate + + + developmental stage + 45 years + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702465 + SAMN31656486 + GSM6720885 + + + + + + + SRR22227685 + GSM6720885_r1 + + + + GSM6720885_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702465 + SAMN31656486 + GSM6720885 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205273 + GSM6720860_r1 + + GSM6720860: Prenatal, sample5, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702464 + GSM6720860 + + + + GSM6720860 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702464 + SAMN31656511 + GSM6720860 + + Prenatal, sample5, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 20.3 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702464 + SAMN31656511 + GSM6720860 + + + + + + + SRR22227686 + GSM6720860_r1 + + + + GSM6720860_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702464 + SAMN31656511 + GSM6720860 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205272 + GSM6720859_r1 + + GSM6720859: Prenatal, sample4, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702463 + GSM6720859 + + + + GSM6720859 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702463 + SAMN31656512 + GSM6720859 + + Prenatal, sample4, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 19.7 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702463 + SAMN31656512 + GSM6720859 + + + + + + + SRR22227687 + GSM6720859_r1 + + + + GSM6720859_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702463 + SAMN31656512 + GSM6720859 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205271 + GSM6720858_r1 + + GSM6720858: Prenatal, sample4, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702462 + GSM6720858 + + + + GSM6720858 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702462 + SAMN31656513 + GSM6720858 + + Prenatal, sample4, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 19.7 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702462 + SAMN31656513 + GSM6720858 + + + + + + + SRR22227688 + GSM6720858_r1 + + + + GSM6720858_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702462 + SAMN31656513 + GSM6720858 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205270 + GSM6720857_r1 + + GSM6720857: Prenatal, sample3, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702461 + GSM6720857 + + + + GSM6720857 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702461 + SAMN31656514 + GSM6720857 + + Prenatal, sample3, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 19 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702461 + SAMN31656514 + GSM6720857 + + + + + + + SRR22227689 + GSM6720857_r1 + + + + GSM6720857_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702461 + SAMN31656514 + GSM6720857 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205269 + GSM6720856_r1 + + GSM6720856: Prenatal, sample3, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702460 + GSM6720856 + + + + GSM6720856 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702460 + SAMN31656515 + GSM6720856 + + Prenatal, sample3, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 19 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702460 + SAMN31656515 + GSM6720856 + + + + + + + SRR22227690 + GSM6720856_r1 + + + + GSM6720856_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702460 + SAMN31656515 + GSM6720856 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205268 + GSM6720855_r1 + + GSM6720855: Prenatal, sample2, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702459 + GSM6720855 + + + + GSM6720855 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702459 + SAMN31656516 + GSM6720855 + + Prenatal, sample2, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 18 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702459 + SAMN31656516 + GSM6720855 + + + + + + + SRR22227691 + GSM6720855_r1 + + + + GSM6720855_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702459 + SAMN31656516 + GSM6720855 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205267 + GSM6720854_r1 + + GSM6720854: Prenatal, sample2, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702458 + GSM6720854 + + + + GSM6720854 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702458 + SAMN31656517 + GSM6720854 + + Prenatal, sample2, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 18 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702458 + SAMN31656517 + GSM6720854 + + + + + + + SRR22227692 + GSM6720854_r1 + + + + GSM6720854_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702458 + SAMN31656517 + GSM6720854 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205266 + GSM6720853_r1 + + GSM6720853: Prenatal, sample1, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702457 + GSM6720853 + + + + GSM6720853 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702457 + SAMN31656518 + GSM6720853 + + Prenatal, sample1, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 17 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702457 + SAMN31656518 + GSM6720853 + + + + + + + SRR22227693 + GSM6720853_r1 + + + + GSM6720853_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702457 + SAMN31656518 + GSM6720853 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205265 + GSM6720884_r1 + + GSM6720884: Adult, sample2, neocortex; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702456 + GSM6720884 + + + + GSM6720884 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702456 + SAMN31656487 + GSM6720884 + + Adult, sample2, neocortex + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, neocortex + + + tissue + Brain, neocortex + + + developmental stage + 45 years + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702456 + SAMN31656487 + GSM6720884 + + + + + + + SRR22227694 + GSM6720884_r1 + + + + GSM6720884_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702456 + SAMN31656487 + GSM6720884 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205264 + GSM6720883_r1 + + GSM6720883: Adult, sample1, SVZ+caudate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702455 + GSM6720883 + + + + GSM6720883 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702455 + SAMN31656488 + GSM6720883 + + Adult, sample1, SVZ+caudate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, svz+caudate + + + tissue + Brain, svz+caudate + + + developmental stage + 28 years + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702455 + SAMN31656488 + GSM6720883 + + + + + + + SRR22227695 + GSM6720883_r1 + + + + GSM6720883_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702455 + SAMN31656488 + GSM6720883 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205263 + GSM6720882_r1 + + GSM6720882: Adult, sample1, neocortex; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702454 + GSM6720882 + + + + GSM6720882 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702454 + SAMN31656489 + GSM6720882 + + Adult, sample1, neocortex + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, neocortex + + + tissue + Brain, neocortex + + + developmental stage + 28 years + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702454 + SAMN31656489 + GSM6720882 + + + + + + + SRR22227696 + GSM6720882_r1 + + + + GSM6720882_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702454 + SAMN31656489 + GSM6720882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205262 + GSM6720881_r1 + + GSM6720881: Prenatal, sample15, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702453 + GSM6720881 + + + + GSM6720881 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702453 + SAMN31656490 + GSM6720881 + + Prenatal, sample15, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 38.3 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702453 + SAMN31656490 + GSM6720881 + + + + + + + SRR22227697 + GSM6720881_r1 + + + + GSM6720881_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702453 + SAMN31656490 + GSM6720881 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205261 + GSM6720880_r1 + + GSM6720880: Prenatal, sample15, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702452 + GSM6720880 + + + + GSM6720880 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702452 + SAMN31656491 + GSM6720880 + + Prenatal, sample15, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 38.3 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702452 + SAMN31656491 + GSM6720880 + + + + + + + SRR22227698 + GSM6720880_r1 + + + + GSM6720880_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702452 + SAMN31656491 + GSM6720880 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205260 + GSM6720879_r1 + + GSM6720879: Prenatal, sample14, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702451 + GSM6720879 + + + + GSM6720879 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702451 + SAMN31656492 + GSM6720879 + + Prenatal, sample14, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 33.2 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702451 + SAMN31656492 + GSM6720879 + + + + + + + SRR22227699 + GSM6720879_r1 + + + + GSM6720879_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702451 + SAMN31656492 + GSM6720879 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205259 + GSM6720878_r1 + + GSM6720878: Prenatal, sample14, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702450 + GSM6720878 + + + + GSM6720878 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702450 + SAMN31656493 + GSM6720878 + + Prenatal, sample14, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 33.2 weeks gestation + + + Sex + male + + + treatment + postmortem, non-pathological + + + + + + + SRS15702450 + SAMN31656493 + GSM6720878 + + + + + + + SRR22227700 + GSM6720878_r1 + + + + GSM6720878_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702450 + SAMN31656493 + GSM6720878 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205258 + GSM6720877_r1 + + GSM6720877: Prenatal, sample13, germinal matrix; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702449 + GSM6720877 + + + + GSM6720877 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702449 + SAMN31656494 + GSM6720877 + + Prenatal, sample13, germinal matrix + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, germinal matrix + + + tissue + Brain, germinal matrix + + + developmental stage + 32.8 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702449 + SAMN31656494 + GSM6720877 + + + + + + + SRR22227701 + GSM6720877_r1 + + + + GSM6720877_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702449 + SAMN31656494 + GSM6720877 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18205257 + GSM6720852_r1 + + GSM6720852: Prenatal, sample1, cortical plate; Homo sapiens; RNA-Seq + + + SRP406822 + PRJNA899373 + + + + + + + SRS15702448 + GSM6720852 + + + + GSM6720852 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3' gene expression (3' GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers. P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1538276 + SUB12273343 + + + + Pathology, Icahn School of Medicine at Mount Sinai + +
+ 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B + NEW YORK + NY + USA +
+ + Nadejda + Tsankova + + + + + + SRP406822 + PRJNA899373 + GSE217511 + + + Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development + + Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors. Overall design: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex. + GSE217511 + + + + + pubmed + 36509746 + + + + + + + SRS15702448 + SAMN31656519 + GSM6720852 + + Prenatal, sample1, cortical plate + + 9606 + Homo sapiens + + + + + bioproject + 899373 + + + + + + + source_name + Brain, cortical plate + + + tissue + Brain, cortical plate + + + developmental stage + 17 weeks gestation + + + Sex + female + + + treatment + postmortem, non-pathological + + + + + + + SRS15702448 + SAMN31656519 + GSM6720852 + + + + + + + SRR22227702 + GSM6720852_r1 + + + + GSM6720852_r1 + + + + + assembly + GRCh38 + + + intentional_duplicate + + + + + + + SRS15702448 + SAMN31656519 + GSM6720852 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE218316.xml b/tests/data/GSE218316.xml new file mode 100644 index 0000000..9ed0b6e --- /dev/null +++ b/tests/data/GSE218316.xml @@ -0,0 +1,1134 @@ + + + + + + + SRX18307134 + GSM6740283_r1 + + GSM6740283: Donor 3 - 72 hours treatment; Homo sapiens; RNA-Seq + + + SRP408608 + PRJNA903151 + + + + + + + SRS15797788 + GSM6740283 + + + + GSM6740283 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend). Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1543480 + SUB12298722 + + + + Islet lab, Internal Medicine, Leiden University Medical Center + +
+ Albinusdreef 2 + Leiden + FN + Netherlands +
+ + Françoise + Carlotti + + + + + + SRP408608 + PRJNA903151 + GSE218316 + + + Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. + + Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions. Overall design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 µM), IL-1ß (1 ng/ml) and/or IFN? (1000 U/ml), IFNa (2000 U/ml), hydrogen peroxide (H2O2, 50 µM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h + GSE218316 + + + + + pubmed + 37581620 + + + + + pubmed + 37924378 + + + + + pubmed + 39499224 + + + + + pubmed + 40471239 + + + + + + + SRS15797788 + SAMN31785789 + GSM6740283 + + Donor 3 - 72 hours treatment + + 9606 + Homo sapiens + + + + + bioproject + 903151 + + + + + + + source_name + Pancreatic islets + + + disease state + Healthy - non diabetic + + + gender + male + + + age + 58 + + + time + 72h + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15797788 + SAMN31785789 + GSM6740283 + + + + + + + SRR22334306 + GSM6740283_r1 + + + + GSM6740283_r1 + + + + + + SRS15797788 + SAMN31785789 + GSM6740283 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18307133 + GSM6740282_r1 + + GSM6740282: Donor 3 - 24 hours treatment; Homo sapiens; RNA-Seq + + + SRP408608 + PRJNA903151 + + + + + + + SRS15797787 + GSM6740282 + + + + GSM6740282 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend). Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1543480 + SUB12298722 + + + + Islet lab, Internal Medicine, Leiden University Medical Center + +
+ Albinusdreef 2 + Leiden + FN + Netherlands +
+ + Françoise + Carlotti + + + + + + SRP408608 + PRJNA903151 + GSE218316 + + + Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. + + Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions. Overall design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 µM), IL-1ß (1 ng/ml) and/or IFN? (1000 U/ml), IFNa (2000 U/ml), hydrogen peroxide (H2O2, 50 µM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h + GSE218316 + + + + + pubmed + 37581620 + + + + + pubmed + 37924378 + + + + + pubmed + 39499224 + + + + + pubmed + 40471239 + + + + + + + SRS15797787 + SAMN31785790 + GSM6740282 + + Donor 3 - 24 hours treatment + + 9606 + Homo sapiens + + + + + bioproject + 903151 + + + + + + + source_name + Pancreatic islets + + + disease state + Healthy - non diabetic + + + gender + male + + + age + 58 + + + time + 24h + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15797787 + SAMN31785790 + GSM6740282 + + + + + + + SRR22334307 + GSM6740282_r1 + + + + GSM6740282_r1 + + + + + + SRS15797787 + SAMN31785790 + GSM6740282 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18307132 + GSM6740280_r1 + + GSM6740280: Donor 2 - 72 hours treatment; Homo sapiens; RNA-Seq + + + SRP408608 + PRJNA903151 + + + + + + + SRS15797785 + GSM6740280 + + + + GSM6740280 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend). Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1543480 + SUB12298722 + + + + Islet lab, Internal Medicine, Leiden University Medical Center + +
+ Albinusdreef 2 + Leiden + FN + Netherlands +
+ + Françoise + Carlotti + + + + + + SRP408608 + PRJNA903151 + GSE218316 + + + Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. + + Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions. Overall design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 µM), IL-1ß (1 ng/ml) and/or IFN? (1000 U/ml), IFNa (2000 U/ml), hydrogen peroxide (H2O2, 50 µM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h + GSE218316 + + + + + pubmed + 37581620 + + + + + pubmed + 37924378 + + + + + pubmed + 39499224 + + + + + pubmed + 40471239 + + + + + + + SRS15797785 + SAMN31785791 + GSM6740280 + + Donor 2 - 72 hours treatment + + 9606 + Homo sapiens + + + + + bioproject + 903151 + + + + + + + source_name + Pancreatic islets + + + disease state + Healthy - non diabetic + + + gender + male + + + age + 55 + + + time + 72h + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15797785 + SAMN31785791 + GSM6740280 + + + + + + + SRR22334308 + GSM6740280_r1 + + + + GSM6740280_r1 + + + + + loader + fastq-load.py + + + + + + SRS15797785 + SAMN31785791 + GSM6740280 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18307131 + GSM6740279_r1 + + GSM6740279: Donor 2 - 24 hours treatment; Homo sapiens; RNA-Seq + + + SRP408608 + PRJNA903151 + + + + + + + SRS15797786 + GSM6740279 + + + + GSM6740279 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend). Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1543480 + SUB12298722 + + + + Islet lab, Internal Medicine, Leiden University Medical Center + +
+ Albinusdreef 2 + Leiden + FN + Netherlands +
+ + Françoise + Carlotti + + + + + + SRP408608 + PRJNA903151 + GSE218316 + + + Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. + + Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions. Overall design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 µM), IL-1ß (1 ng/ml) and/or IFN? (1000 U/ml), IFNa (2000 U/ml), hydrogen peroxide (H2O2, 50 µM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h + GSE218316 + + + + + pubmed + 37581620 + + + + + pubmed + 37924378 + + + + + pubmed + 39499224 + + + + + pubmed + 40471239 + + + + + + + SRS15797786 + SAMN31785792 + GSM6740279 + + Donor 2 - 24 hours treatment + + 9606 + Homo sapiens + + + + + bioproject + 903151 + + + + + + + source_name + Pancreatic islets + + + disease state + Healthy - non diabetic + + + gender + male + + + age + 55 + + + time + 24h + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15797786 + SAMN31785792 + GSM6740279 + + + + + + + SRR22334309 + GSM6740279_r1 + + + + GSM6740279_r1 + + + + + loader + fastq-load.py + + + + + + SRS15797786 + SAMN31785792 + GSM6740279 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18307130 + GSM6740278_r1 + + GSM6740278: Donor 1 - 24 hours treatment; Homo sapiens; RNA-Seq + + + SRP408608 + PRJNA903151 + + + + + + + SRS15797784 + GSM6740278 + + + + GSM6740278 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + After treatment islets were dispersed into single cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material. Islets exposed to the different treatments were multiplexed per timepoint and donor using cell hashing. Briefly, each treated islet cell suspension was incubated with a pool of barcoded antibodies directed against B2M and CD298 (TotalSeq-A BioLegend). Labeled cell suspensions were pooled per donor and time point and processed for single-cell mRNA sequencing. Prior to loading the 10x Chromium controller, the pooled cell suspensions were counted to assess cell integrity and concentration. Cell suspensions were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1543480 + SUB12298722 + + + + Islet lab, Internal Medicine, Leiden University Medical Center + +
+ Albinusdreef 2 + Leiden + FN + Netherlands +
+ + Françoise + Carlotti + + + + + + SRP408608 + PRJNA903151 + GSE218316 + + + Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. + + Diabetes mellitus (DM) is a chronic disease associated with elevated blood glucose level and resulting from a loss of functional beta-cell mass. The goal of this study is to investigate the response of human pancreatic cells to pathophysiological conditions associated with beta-cell dysfunction, ultimately to identify molecular mechanisms contributing to the development of diabetes. Isolated primary human islets from three non-diabetic donors were exposed in vitro to pro-inflammatory, oxidative, metabolic and endoplasmic reticulum stress for up to 3 days. Subsequently the cells were processed for single-cell RNA sequencing (scRNA-seq). Analysis of the dataset revealed both common and specific molecular response of each pancreatic cell type to the various stress conditions. Overall design: Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 µM), IL-1ß (1 ng/ml) and/or IFN? (1000 U/ml), IFNa (2000 U/ml), hydrogen peroxide (H2O2, 50 µM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h + GSE218316 + + + + + pubmed + 37581620 + + + + + pubmed + 37924378 + + + + + pubmed + 39499224 + + + + + pubmed + 40471239 + + + + + + + SRS15797784 + SAMN31785793 + GSM6740278 + + Donor 1 - 24 hours treatment + + 9606 + Homo sapiens + + + + + bioproject + 903151 + + + + + + + source_name + Pancreatic islets + + + disease state + Healthy - non diabetic + + + time + 24h + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS15797784 + SAMN31785793 + GSM6740278 + + + + + + + SRR22334310 + GSM6740278_r1 + + + + GSM6740278_r1 + + + + + loader + fastq-load.py + + + + + + SRS15797784 + SAMN31785793 + GSM6740278 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE218572.xml b/tests/data/GSE218572.xml new file mode 100644 index 0000000..cd2f4bb --- /dev/null +++ b/tests/data/GSE218572.xml @@ -0,0 +1,23990 @@ + + + + + + + SRX19119346 + + GSM6752752: 12-week TH Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552965 + GSM6752752 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752752 + + + + + + + GEO Accession + GSM6752752 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552965 + SAMN32855628 + GSM6752752 + + 12-week TH Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552965 + SAMN32855628 + GSM6752752 + + + + + + + SRR23168790 + GSM6752752_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552965 + SAMN32855628 + GSM6752752 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168791 + GSM6752752_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552965 + SAMN32855628 + GSM6752752 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119344 + + GSM6752751: 12-week TH Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552964 + GSM6752751 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752751 + + + + + + + GEO Accession + GSM6752751 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552964 + SAMN32855627 + GSM6752751 + + 12-week TH Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552964 + SAMN32855627 + GSM6752751 + + + + + + + SRR23168788 + GSM6752751_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552964 + SAMN32855627 + GSM6752751 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168789 + GSM6752751_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552964 + SAMN32855627 + GSM6752751 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119342 + + GSM6752750: 12-week TH Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552963 + GSM6752750 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752750 + + + + + + + GEO Accession + GSM6752750 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552963 + SAMN32855626 + GSM6752750 + + 12-week TH Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552963 + SAMN32855626 + GSM6752750 + + + + + + + SRR23168786 + GSM6752750_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552963 + SAMN32855626 + GSM6752750 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168787 + GSM6752750_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552963 + SAMN32855626 + GSM6752750 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119340 + + GSM6752717: 12-week PFC Grin2a WT snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552960 + GSM6752717 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752717 + + + + + + + GEO Accession + GSM6752717 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552960 + SAMN32855580 + GSM6752717 + + 12-week PFC Grin2a WT snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552960 + SAMN32855580 + GSM6752717 + + + + + + + SRR23168720 + GSM6752717_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552960 + SAMN32855580 + GSM6752717 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168721 + GSM6752717_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552960 + SAMN32855580 + GSM6752717 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119338 + + GSM6752716: 12-week PFC Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552962 + GSM6752716 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752716 + + + + + + + GEO Accession + GSM6752716 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552962 + SAMN32855579 + GSM6752716 + + 12-week PFC Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552962 + SAMN32855579 + GSM6752716 + + + + + + + SRR23168718 + GSM6752716_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552962 + SAMN32855579 + GSM6752716 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168719 + GSM6752716_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552962 + SAMN32855579 + GSM6752716 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119336 + + GSM6752715: 12-week PFC Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552959 + GSM6752715 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752715 + + + + + + + GEO Accession + GSM6752715 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552959 + SAMN32855578 + GSM6752715 + + 12-week PFC Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552959 + SAMN32855578 + GSM6752715 + + + + + + + SRR23168716 + GSM6752715_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552959 + SAMN32855578 + GSM6752715 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168717 + GSM6752715_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552959 + SAMN32855578 + GSM6752715 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119334 + + GSM6752714: 12-week PFC Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552961 + GSM6752714 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752714 + + + + + + + GEO Accession + GSM6752714 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552961 + SAMN32855577 + GSM6752714 + + 12-week PFC Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552961 + SAMN32855577 + GSM6752714 + + + + + + + SRR23168714 + GSM6752714_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552961 + SAMN32855577 + GSM6752714 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168715 + GSM6752714_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552961 + SAMN32855577 + GSM6752714 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119332 + + GSM6752713: 12-week PFC Grin2a -/- snRNA-seq Sample5; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552958 + GSM6752713 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752713 + + + + + + + GEO Accession + GSM6752713 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552958 + SAMN32855576 + GSM6752713 + + 12-week PFC Grin2a -/- snRNA-seq Sample5 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552958 + SAMN32855576 + GSM6752713 + + + + + + + SRR23168712 + GSM6752713_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552958 + SAMN32855576 + GSM6752713 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168713 + GSM6752713_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552958 + SAMN32855576 + GSM6752713 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119330 + + GSM6752712: 12-week PFC Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552957 + GSM6752712 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752712 + + + + + + + GEO Accession + GSM6752712 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552957 + SAMN32855575 + GSM6752712 + + 12-week PFC Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552957 + SAMN32855575 + GSM6752712 + + + + + + + SRR23168710 + GSM6752712_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552957 + SAMN32855575 + GSM6752712 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168711 + GSM6752712_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552957 + SAMN32855575 + GSM6752712 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119328 + + GSM6752711: 12-week PFC Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552956 + GSM6752711 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752711 + + + + + + + GEO Accession + GSM6752711 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552956 + SAMN32855574 + GSM6752711 + + 12-week PFC Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552956 + SAMN32855574 + GSM6752711 + + + + + + + SRR23168708 + GSM6752711_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552956 + SAMN32855574 + GSM6752711 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168709 + GSM6752711_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552956 + SAMN32855574 + GSM6752711 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119326 + + GSM6752710: 12-week PFC Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552955 + GSM6752710 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752710 + + + + + + + GEO Accession + GSM6752710 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552955 + SAMN32855573 + GSM6752710 + + 12-week PFC Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552955 + SAMN32855573 + GSM6752710 + + + + + + + SRR23168706 + GSM6752710_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552955 + SAMN32855573 + GSM6752710 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168707 + GSM6752710_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552955 + SAMN32855573 + GSM6752710 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119324 + + GSM6752709: 12-week PFC Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552953 + GSM6752709 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752709 + + + + + + + GEO Accession + GSM6752709 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552953 + SAMN32855572 + GSM6752709 + + 12-week PFC Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552953 + SAMN32855572 + GSM6752709 + + + + + + + SRR23168704 + GSM6752709_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552953 + SAMN32855572 + GSM6752709 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168705 + GSM6752709_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552953 + SAMN32855572 + GSM6752709 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119322 + + GSM6752708: 12-week PFC Grin2a +/- snRNA-seq Sample5; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552954 + GSM6752708 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752708 + + + + + + + GEO Accession + GSM6752708 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552954 + SAMN32855571 + GSM6752708 + + 12-week PFC Grin2a +/- snRNA-seq Sample5 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552954 + SAMN32855571 + GSM6752708 + + + + + + + SRR23168702 + GSM6752708_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552954 + SAMN32855571 + GSM6752708 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168703 + GSM6752708_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552954 + SAMN32855571 + GSM6752708 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119319 + + GSM6752707: 12-week PFC Grin2a +/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552951 + GSM6752707 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752707 + + + + + + + GEO Accession + GSM6752707 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552951 + SAMN32855570 + GSM6752707 + + 12-week PFC Grin2a +/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552951 + SAMN32855570 + GSM6752707 + + + + + + + SRR23168700 + GSM6752707_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552951 + SAMN32855570 + GSM6752707 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168701 + GSM6752707_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552951 + SAMN32855570 + GSM6752707 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119316 + + GSM6752706: 12-week PFC Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552952 + GSM6752706 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752706 + + + + + + + GEO Accession + GSM6752706 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552952 + SAMN32855569 + GSM6752706 + + 12-week PFC Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552952 + SAMN32855569 + GSM6752706 + + + + + + + SRR23168698 + GSM6752706_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552952 + SAMN32855569 + GSM6752706 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168699 + GSM6752706_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552952 + SAMN32855569 + GSM6752706 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119314 + + GSM6752705: 12-week PFC Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552950 + GSM6752705 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752705 + + + + + + + GEO Accession + GSM6752705 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552950 + SAMN32855568 + GSM6752705 + + 12-week PFC Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552950 + SAMN32855568 + GSM6752705 + + + + + + + SRR23168696 + GSM6752705_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552950 + SAMN32855568 + GSM6752705 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168697 + GSM6752705_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552950 + SAMN32855568 + GSM6752705 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119312 + + GSM6752704: 12-week PFC Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552949 + GSM6752704 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752704 + + + + + + + GEO Accession + GSM6752704 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552949 + SAMN32855567 + GSM6752704 + + 12-week PFC Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552949 + SAMN32855567 + GSM6752704 + + + + + + + SRR23168694 + GSM6752704_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552949 + SAMN32855567 + GSM6752704 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168695 + GSM6752704_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552949 + SAMN32855567 + GSM6752704 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119310 + + GSM6752703: 4-week PFC Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552947 + GSM6752703 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752703 + + + + + + + GEO Accession + GSM6752703 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552947 + SAMN32855566 + GSM6752703 + + 4-week PFC Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552947 + SAMN32855566 + GSM6752703 + + + + + + + SRR23168692 + GSM6752703_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552947 + SAMN32855566 + GSM6752703 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168693 + GSM6752703_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552947 + SAMN32855566 + GSM6752703 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119308 + + GSM6752702: 4-week PFC Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552946 + GSM6752702 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752702 + + + + + + + GEO Accession + GSM6752702 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552946 + SAMN32855565 + GSM6752702 + + 4-week PFC Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552946 + SAMN32855565 + GSM6752702 + + + + + + + SRR23168690 + GSM6752702_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552946 + SAMN32855565 + GSM6752702 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168691 + GSM6752702_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552946 + SAMN32855565 + GSM6752702 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119306 + + GSM6752749: 12-week TH Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552948 + GSM6752749 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752749 + + + + + + + GEO Accession + GSM6752749 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552948 + SAMN32855625 + GSM6752749 + + 12-week TH Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552948 + SAMN32855625 + GSM6752749 + + + + + + + SRR23168784 + GSM6752749_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552948 + SAMN32855625 + GSM6752749 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168785 + GSM6752749_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552948 + SAMN32855625 + GSM6752749 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119304 + + GSM6752748: 12-week TH Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552945 + GSM6752748 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752748 + + + + + + + GEO Accession + GSM6752748 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552945 + SAMN32855624 + GSM6752748 + + 12-week TH Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552945 + SAMN32855624 + GSM6752748 + + + + + + + SRR23168782 + GSM6752748_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552945 + SAMN32855624 + GSM6752748 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168783 + GSM6752748_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552945 + SAMN32855624 + GSM6752748 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119302 + + GSM6752747: 12-week TH Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552944 + GSM6752747 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752747 + + + + + + + GEO Accession + GSM6752747 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552944 + SAMN32855623 + GSM6752747 + + 12-week TH Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552944 + SAMN32855623 + GSM6752747 + + + + + + + SRR23168780 + GSM6752747_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552944 + SAMN32855623 + GSM6752747 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168781 + GSM6752747_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552944 + SAMN32855623 + GSM6752747 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119299 + + GSM6752746: 12-week TH Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552943 + GSM6752746 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752746 + + + + + + + GEO Accession + GSM6752746 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552943 + SAMN32855622 + GSM6752746 + + 12-week TH Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552943 + SAMN32855622 + GSM6752746 + + + + + + + SRR23168778 + GSM6752746_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552943 + SAMN32855622 + GSM6752746 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168779 + GSM6752746_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552943 + SAMN32855622 + GSM6752746 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119297 + + GSM6752745: 12-week TH Grin2a +/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552942 + GSM6752745 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752745 + + + + + + + GEO Accession + GSM6752745 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552942 + SAMN32855621 + GSM6752745 + + 12-week TH Grin2a +/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552942 + SAMN32855621 + GSM6752745 + + + + + + + SRR23168776 + GSM6752745_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552942 + SAMN32855621 + GSM6752745 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168777 + GSM6752745_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552942 + SAMN32855621 + GSM6752745 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119295 + + GSM6752744: 12-week TH Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552939 + GSM6752744 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752744 + + + + + + + GEO Accession + GSM6752744 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552939 + SAMN32855620 + GSM6752744 + + 12-week TH Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552939 + SAMN32855620 + GSM6752744 + + + + + + + SRR23168774 + GSM6752744_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552939 + SAMN32855620 + GSM6752744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168775 + GSM6752744_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552939 + SAMN32855620 + GSM6752744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119293 + + GSM6752743: 12-week TH Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552941 + GSM6752743 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752743 + + + + + + + GEO Accession + GSM6752743 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552941 + SAMN32855619 + GSM6752743 + + 12-week TH Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552941 + SAMN32855619 + GSM6752743 + + + + + + + SRR23168772 + GSM6752743_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552941 + SAMN32855619 + GSM6752743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168773 + GSM6752743_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552941 + SAMN32855619 + GSM6752743 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119292 + + GSM6752742: 12-week TH Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552940 + GSM6752742 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752742 + + + + + + + GEO Accession + GSM6752742 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552940 + SAMN32855618 + GSM6752742 + + 12-week TH Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Thalamus + + + tissue + Thalamus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552940 + SAMN32855618 + GSM6752742 + + + + + + + SRR23168770 + GSM6752742_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552940 + SAMN32855618 + GSM6752742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168771 + GSM6752742_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552940 + SAMN32855618 + GSM6752742 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119290 + + GSM6752741: 12-week ST Grin2a WT snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552938 + GSM6752741 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752741 + + + + + + + GEO Accession + GSM6752741 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552938 + SAMN32855617 + GSM6752741 + + 12-week ST Grin2a WT snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552938 + SAMN32855617 + GSM6752741 + + + + + + + SRR23168768 + GSM6752741_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552938 + SAMN32855617 + GSM6752741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168769 + GSM6752741_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552938 + SAMN32855617 + GSM6752741 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119288 + + GSM6752740: 12-week ST Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552937 + GSM6752740 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752740 + + + + + + + GEO Accession + GSM6752740 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552937 + SAMN32855616 + GSM6752740 + + 12-week ST Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552937 + SAMN32855616 + GSM6752740 + + + + + + + SRR23168766 + GSM6752740_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552937 + SAMN32855616 + GSM6752740 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168767 + GSM6752740_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552937 + SAMN32855616 + GSM6752740 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119286 + + GSM6752739: 12-week ST Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552936 + GSM6752739 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752739 + + + + + + + GEO Accession + GSM6752739 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552936 + SAMN32855615 + GSM6752739 + + 12-week ST Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552936 + SAMN32855615 + GSM6752739 + + + + + + + SRR23168764 + GSM6752739_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552936 + SAMN32855615 + GSM6752739 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168765 + GSM6752739_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552936 + SAMN32855615 + GSM6752739 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119284 + + GSM6752738: 12-week ST Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552935 + GSM6752738 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752738 + + + + + + + GEO Accession + GSM6752738 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552935 + SAMN32855614 + GSM6752738 + + 12-week ST Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552935 + SAMN32855614 + GSM6752738 + + + + + + + SRR23168762 + GSM6752738_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552935 + SAMN32855614 + GSM6752738 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168763 + GSM6752738_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552935 + SAMN32855614 + GSM6752738 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119282 + + GSM6752737: 12-week ST Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552934 + GSM6752737 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752737 + + + + + + + GEO Accession + GSM6752737 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552934 + SAMN32855613 + GSM6752737 + + 12-week ST Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552934 + SAMN32855613 + GSM6752737 + + + + + + + SRR23168760 + GSM6752737_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552934 + SAMN32855613 + GSM6752737 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168761 + GSM6752737_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552934 + SAMN32855613 + GSM6752737 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119280 + + GSM6752736: 12-week ST Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552933 + GSM6752736 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752736 + + + + + + + GEO Accession + GSM6752736 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552933 + SAMN32855612 + GSM6752736 + + 12-week ST Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552933 + SAMN32855612 + GSM6752736 + + + + + + + SRR23168758 + GSM6752736_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552933 + SAMN32855612 + GSM6752736 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168759 + GSM6752736_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552933 + SAMN32855612 + GSM6752736 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119278 + + GSM6752735: 12-week ST Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552932 + GSM6752735 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752735 + + + + + + + GEO Accession + GSM6752735 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552932 + SAMN32855611 + GSM6752735 + + 12-week ST Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552932 + SAMN32855611 + GSM6752735 + + + + + + + SRR23168756 + GSM6752735_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552932 + SAMN32855611 + GSM6752735 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168757 + GSM6752735_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552932 + SAMN32855611 + GSM6752735 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119276 + + GSM6752734: 12-week ST Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552931 + GSM6752734 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752734 + + + + + + + GEO Accession + GSM6752734 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552931 + SAMN32855610 + GSM6752734 + + 12-week ST Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552931 + SAMN32855610 + GSM6752734 + + + + + + + SRR23168754 + GSM6752734_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552931 + SAMN32855610 + GSM6752734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168755 + GSM6752734_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552931 + SAMN32855610 + GSM6752734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119274 + + GSM6752701: 4-week PFC Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552930 + GSM6752701 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752701 + + + + + + + GEO Accession + GSM6752701 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552930 + SAMN32855564 + GSM6752701 + + 4-week PFC Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552930 + SAMN32855564 + GSM6752701 + + + + + + + SRR23168688 + GSM6752701_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552930 + SAMN32855564 + GSM6752701 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168689 + GSM6752701_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552930 + SAMN32855564 + GSM6752701 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119272 + + GSM6752700: 4-week PFC Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552929 + GSM6752700 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752700 + + + + + + + GEO Accession + GSM6752700 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552929 + SAMN32855563 + GSM6752700 + + 4-week PFC Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552929 + SAMN32855563 + GSM6752700 + + + + + + + SRR23168686 + GSM6752700_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552929 + SAMN32855563 + GSM6752700 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168687 + GSM6752700_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552929 + SAMN32855563 + GSM6752700 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119270 + + GSM6752699: 4-week PFC Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552928 + GSM6752699 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752699 + + + + + + + GEO Accession + GSM6752699 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552928 + SAMN32855562 + GSM6752699 + + 4-week PFC Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552928 + SAMN32855562 + GSM6752699 + + + + + + + SRR23168684 + GSM6752699_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552928 + SAMN32855562 + GSM6752699 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168685 + GSM6752699_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552928 + SAMN32855562 + GSM6752699 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119268 + + GSM6752698: 4-week PFC Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552927 + GSM6752698 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752698 + + + + + + + GEO Accession + GSM6752698 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552927 + SAMN32855561 + GSM6752698 + + 4-week PFC Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552927 + SAMN32855561 + GSM6752698 + + + + + + + SRR23168682 + GSM6752698_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552927 + SAMN32855561 + GSM6752698 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168683 + GSM6752698_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552927 + SAMN32855561 + GSM6752698 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119266 + + GSM6752697: 4-week PFC Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552926 + GSM6752697 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752697 + + + + + + + GEO Accession + GSM6752697 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552926 + SAMN32855560 + GSM6752697 + + 4-week PFC Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552926 + SAMN32855560 + GSM6752697 + + + + + + + SRR23168680 + GSM6752697_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552926 + SAMN32855560 + GSM6752697 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168681 + GSM6752697_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552926 + SAMN32855560 + GSM6752697 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119265 + + GSM6752696: 4-week PFC Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552925 + GSM6752696 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752696 + + + + + + + GEO Accession + GSM6752696 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552925 + SAMN32855559 + GSM6752696 + + 4-week PFC Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552925 + SAMN32855559 + GSM6752696 + + + + + + + SRR23168678 + GSM6752696_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552925 + SAMN32855559 + GSM6752696 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168679 + GSM6752696_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552925 + SAMN32855559 + GSM6752696 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119263 + + GSM6752695: 4-week PFC Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552924 + GSM6752695 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752695 + + + + + + + GEO Accession + GSM6752695 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552924 + SAMN32855558 + GSM6752695 + + 4-week PFC Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Prefrontal Cortex + + + tissue + Prefrontal Cortex + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552924 + SAMN32855558 + GSM6752695 + + + + + + + SRR23168676 + GSM6752695_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552924 + SAMN32855558 + GSM6752695 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168677 + GSM6752695_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552924 + SAMN32855558 + GSM6752695 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119262 + + GSM6752694: 12-week HP Grin2a WT snRNA-seq Sample5; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552923 + GSM6752694 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752694 + + + + + + + GEO Accession + GSM6752694 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552923 + SAMN32855557 + GSM6752694 + + 12-week HP Grin2a WT snRNA-seq Sample5 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552923 + SAMN32855557 + GSM6752694 + + + + + + + SRR23168674 + GSM6752694_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552923 + SAMN32855557 + GSM6752694 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168675 + GSM6752694_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552923 + SAMN32855557 + GSM6752694 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119260 + + GSM6752693: 12-week HP Grin2a WT snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552921 + GSM6752693 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752693 + + + + + + + GEO Accession + GSM6752693 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552921 + SAMN32855556 + GSM6752693 + + 12-week HP Grin2a WT snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552921 + SAMN32855556 + GSM6752693 + + + + + + + SRR23168672 + GSM6752693_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552921 + SAMN32855556 + GSM6752693 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168673 + GSM6752693_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552921 + SAMN32855556 + GSM6752693 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119258 + + GSM6752692: 12-week HP Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552922 + GSM6752692 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752692 + + + + + + + GEO Accession + GSM6752692 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552922 + SAMN32855555 + GSM6752692 + + 12-week HP Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552922 + SAMN32855555 + GSM6752692 + + + + + + + SRR23168670 + GSM6752692_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552922 + SAMN32855555 + GSM6752692 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168671 + GSM6752692_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552922 + SAMN32855555 + GSM6752692 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119256 + + GSM6752691: 12-week HP Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552920 + GSM6752691 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752691 + + + + + + + GEO Accession + GSM6752691 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552920 + SAMN32855554 + GSM6752691 + + 12-week HP Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552920 + SAMN32855554 + GSM6752691 + + + + + + + SRR23168668 + GSM6752691_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552920 + SAMN32855554 + GSM6752691 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168669 + GSM6752691_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552920 + SAMN32855554 + GSM6752691 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119254 + + GSM6752690: 12-week HP Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552919 + GSM6752690 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752690 + + + + + + + GEO Accession + GSM6752690 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552919 + SAMN32855553 + GSM6752690 + + 12-week HP Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552919 + SAMN32855553 + GSM6752690 + + + + + + + SRR23168666 + GSM6752690_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552919 + SAMN32855553 + GSM6752690 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168667 + GSM6752690_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552919 + SAMN32855553 + GSM6752690 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119252 + + GSM6752689: 12-week HP Grin2a -/- snRNA-seq Sample5; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552918 + GSM6752689 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752689 + + + + + + + GEO Accession + GSM6752689 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552918 + SAMN32855552 + GSM6752689 + + 12-week HP Grin2a -/- snRNA-seq Sample5 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552918 + SAMN32855552 + GSM6752689 + + + + + + + SRR23168664 + GSM6752689_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552918 + SAMN32855552 + GSM6752689 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168665 + GSM6752689_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552918 + SAMN32855552 + GSM6752689 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119250 + + GSM6752688: 12-week HP Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552916 + GSM6752688 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752688 + + + + + + + GEO Accession + GSM6752688 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552916 + SAMN32855551 + GSM6752688 + + 12-week HP Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552916 + SAMN32855551 + GSM6752688 + + + + + + + SRR23168662 + GSM6752688_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552916 + SAMN32855551 + GSM6752688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168663 + GSM6752688_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552916 + SAMN32855551 + GSM6752688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119248 + + GSM6752687: 12-week HP Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552915 + GSM6752687 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752687 + + + + + + + GEO Accession + GSM6752687 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552915 + SAMN32855550 + GSM6752687 + + 12-week HP Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552915 + SAMN32855550 + GSM6752687 + + + + + + + SRR23168660 + GSM6752687_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552915 + SAMN32855550 + GSM6752687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168661 + GSM6752687_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552915 + SAMN32855550 + GSM6752687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119246 + + GSM6752686: 12-week HP Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552917 + GSM6752686 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752686 + + + + + + + GEO Accession + GSM6752686 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552917 + SAMN32855549 + GSM6752686 + + 12-week HP Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552917 + SAMN32855549 + GSM6752686 + + + + + + + SRR23168658 + GSM6752686_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552917 + SAMN32855549 + GSM6752686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168659 + GSM6752686_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552917 + SAMN32855549 + GSM6752686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119244 + + GSM6752733: 12-week ST Grin2a +/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552914 + GSM6752733 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752733 + + + + + + + GEO Accession + GSM6752733 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552914 + SAMN32855609 + GSM6752733 + + 12-week ST Grin2a +/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552914 + SAMN32855609 + GSM6752733 + + + + + + + SRR23168752 + GSM6752733_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552914 + SAMN32855609 + GSM6752733 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168753 + GSM6752733_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552914 + SAMN32855609 + GSM6752733 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119242 + + GSM6752732: 12-week ST Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552912 + GSM6752732 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752732 + + + + + + + GEO Accession + GSM6752732 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552912 + SAMN32855608 + GSM6752732 + + 12-week ST Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552912 + SAMN32855608 + GSM6752732 + + + + + + + SRR23168750 + GSM6752732_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552912 + SAMN32855608 + GSM6752732 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168751 + GSM6752732_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552912 + SAMN32855608 + GSM6752732 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119240 + + GSM6752731: 12-week ST Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552913 + GSM6752731 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752731 + + + + + + + GEO Accession + GSM6752731 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552913 + SAMN32855607 + GSM6752731 + + 12-week ST Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552913 + SAMN32855607 + GSM6752731 + + + + + + + SRR23168748 + GSM6752731_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552913 + SAMN32855607 + GSM6752731 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168749 + GSM6752731_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552913 + SAMN32855607 + GSM6752731 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119238 + + GSM6752730: 12-week ST Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552911 + GSM6752730 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752730 + + + + + + + GEO Accession + GSM6752730 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552911 + SAMN32855606 + GSM6752730 + + 12-week ST Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Striatum + + + tissue + Striatum + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552911 + SAMN32855606 + GSM6752730 + + + + + + + SRR23168746 + GSM6752730_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552911 + SAMN32855606 + GSM6752730 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168747 + GSM6752730_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552911 + SAMN32855606 + GSM6752730 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119236 + + GSM6752729: 12-week SSC Grin2a WT snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552910 + GSM6752729 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752729 + + + + + + + GEO Accession + GSM6752729 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552910 + SAMN32855605 + GSM6752729 + + 12-week SSC Grin2a WT snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552910 + SAMN32855605 + GSM6752729 + + + + + + + SRR23168744 + GSM6752729_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552910 + SAMN32855605 + GSM6752729 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168745 + GSM6752729_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552910 + SAMN32855605 + GSM6752729 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119234 + + GSM6752728: 12-week SSC Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552909 + GSM6752728 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752728 + + + + + + + GEO Accession + GSM6752728 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552909 + SAMN32855604 + GSM6752728 + + 12-week SSC Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552909 + SAMN32855604 + GSM6752728 + + + + + + + SRR23168742 + GSM6752728_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552909 + SAMN32855604 + GSM6752728 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168743 + GSM6752728_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552909 + SAMN32855604 + GSM6752728 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119232 + + GSM6752727: 12-week SSC Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552907 + GSM6752727 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752727 + + + + + + + GEO Accession + GSM6752727 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552907 + SAMN32855603 + GSM6752727 + + 12-week SSC Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552907 + SAMN32855603 + GSM6752727 + + + + + + + SRR23168740 + GSM6752727_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552907 + SAMN32855603 + GSM6752727 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168741 + GSM6752727_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552907 + SAMN32855603 + GSM6752727 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119230 + + GSM6752726: 12-week SSC Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552908 + GSM6752726 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752726 + + + + + + + GEO Accession + GSM6752726 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552908 + SAMN32855602 + GSM6752726 + + 12-week SSC Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + WT + + + age + 12-week + + + + + + + SRS16552908 + SAMN32855602 + GSM6752726 + + + + + + + SRR23168738 + GSM6752726_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552908 + SAMN32855602 + GSM6752726 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168739 + GSM6752726_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552908 + SAMN32855602 + GSM6752726 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119228 + + GSM6752725: 12-week SSC Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552905 + GSM6752725 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752725 + + + + + + + GEO Accession + GSM6752725 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552905 + SAMN32855601 + GSM6752725 + + 12-week SSC Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552905 + SAMN32855601 + GSM6752725 + + + + + + + SRR23168736 + GSM6752725_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552905 + SAMN32855601 + GSM6752725 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168737 + GSM6752725_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552905 + SAMN32855601 + GSM6752725 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119226 + + GSM6752724: 12-week SSC Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552906 + GSM6752724 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752724 + + + + + + + GEO Accession + GSM6752724 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552906 + SAMN32855600 + GSM6752724 + + 12-week SSC Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552906 + SAMN32855600 + GSM6752724 + + + + + + + SRR23168734 + GSM6752724_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552906 + SAMN32855600 + GSM6752724 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168735 + GSM6752724_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552906 + SAMN32855600 + GSM6752724 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119224 + + GSM6752723: 12-week SSC Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552904 + GSM6752723 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752723 + + + + + + + GEO Accession + GSM6752723 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552904 + SAMN32855586 + GSM6752723 + + 12-week SSC Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552904 + SAMN32855586 + GSM6752723 + + + + + + + SRR23168732 + GSM6752723_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552904 + SAMN32855586 + GSM6752723 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168733 + GSM6752723_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552904 + SAMN32855586 + GSM6752723 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119222 + + GSM6752722: 12-week SSC Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552903 + GSM6752722 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752722 + + + + + + + GEO Accession + GSM6752722 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552903 + SAMN32855585 + GSM6752722 + + 12-week SSC Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552903 + SAMN32855585 + GSM6752722 + + + + + + + SRR23168730 + GSM6752722_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552903 + SAMN32855585 + GSM6752722 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168731 + GSM6752722_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552903 + SAMN32855585 + GSM6752722 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119220 + + GSM6752721: 12-week SSC Grin2a +/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552901 + GSM6752721 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752721 + + + + + + + GEO Accession + GSM6752721 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552901 + SAMN32855584 + GSM6752721 + + 12-week SSC Grin2a +/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552901 + SAMN32855584 + GSM6752721 + + + + + + + SRR23168728 + GSM6752721_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552901 + SAMN32855584 + GSM6752721 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168729 + GSM6752721_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552901 + SAMN32855584 + GSM6752721 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119218 + + GSM6752720: 12-week SSC Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552902 + GSM6752720 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752720 + + + + + + + GEO Accession + GSM6752720 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552902 + SAMN32855583 + GSM6752720 + + 12-week SSC Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552902 + SAMN32855583 + GSM6752720 + + + + + + + SRR23168726 + GSM6752720_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552902 + SAMN32855583 + GSM6752720 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168727 + GSM6752720_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552902 + SAMN32855583 + GSM6752720 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119216 + + GSM6752719: 12-week SSC Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552899 + GSM6752719 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752719 + + + + + + + GEO Accession + GSM6752719 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552899 + SAMN32855582 + GSM6752719 + + 12-week SSC Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552899 + SAMN32855582 + GSM6752719 + + + + + + + SRR23168724 + GSM6752719_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552899 + SAMN32855582 + GSM6752719 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168725 + GSM6752719_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552899 + SAMN32855582 + GSM6752719 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119214 + + GSM6752718: 12-week SSC Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552900 + GSM6752718 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752718 + + + + + + + GEO Accession + GSM6752718 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552900 + SAMN32855581 + GSM6752718 + + 12-week SSC Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Somatosensory Cortex + + + tissue + Somatosensory Cortex + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552900 + SAMN32855581 + GSM6752718 + + + + + + + SRR23168722 + GSM6752718_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552900 + SAMN32855581 + GSM6752718 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168723 + GSM6752718_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552900 + SAMN32855581 + GSM6752718 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119212 + + GSM6752685: 12-week HP Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552897 + GSM6752685 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752685 + + + + + + + GEO Accession + GSM6752685 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552897 + SAMN32855548 + GSM6752685 + + 12-week HP Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 12-week + + + + + + + SRS16552897 + SAMN32855548 + GSM6752685 + + + + + + + SRR23168656 + GSM6752685_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552897 + SAMN32855548 + GSM6752685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168657 + GSM6752685_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552897 + SAMN32855548 + GSM6752685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119210 + + GSM6752684: 12-week HP Grin2a +/- snRNA-seq Sample5; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552898 + GSM6752684 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752684 + + + + + + + GEO Accession + GSM6752684 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552898 + SAMN32855547 + GSM6752684 + + 12-week HP Grin2a +/- snRNA-seq Sample5 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552898 + SAMN32855547 + GSM6752684 + + + + + + + SRR23168654 + GSM6752684_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552898 + SAMN32855547 + GSM6752684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168655 + GSM6752684_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552898 + SAMN32855547 + GSM6752684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119209 + + GSM6752683: 12-week HP Grin2a +/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552896 + GSM6752683 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752683 + + + + + + + GEO Accession + GSM6752683 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552896 + SAMN32855546 + GSM6752683 + + 12-week HP Grin2a +/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552896 + SAMN32855546 + GSM6752683 + + + + + + + SRR23168652 + GSM6752683_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552896 + SAMN32855546 + GSM6752683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168653 + GSM6752683_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552896 + SAMN32855546 + GSM6752683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119208 + + GSM6752682: 12-week HP Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552894 + GSM6752682 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752682 + + + + + + + GEO Accession + GSM6752682 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552894 + SAMN32855545 + GSM6752682 + + 12-week HP Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552894 + SAMN32855545 + GSM6752682 + + + + + + + SRR23168650 + GSM6752682_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552894 + SAMN32855545 + GSM6752682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168651 + GSM6752682_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552894 + SAMN32855545 + GSM6752682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119207 + + GSM6752681: 12-week HP Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552895 + GSM6752681 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752681 + + + + + + + GEO Accession + GSM6752681 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552895 + SAMN32855544 + GSM6752681 + + 12-week HP Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552895 + SAMN32855544 + GSM6752681 + + + + + + + SRR23168648 + GSM6752681_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552895 + SAMN32855544 + GSM6752681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168649 + GSM6752681_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552895 + SAMN32855544 + GSM6752681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119206 + + GSM6752680: 12-week HP Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552893 + GSM6752680 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752680 + + + + + + + GEO Accession + GSM6752680 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552893 + SAMN32855543 + GSM6752680 + + 12-week HP Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 12-week + + + + + + + SRS16552893 + SAMN32855543 + GSM6752680 + + + + + + + SRR23168646 + GSM6752680_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552893 + SAMN32855543 + GSM6752680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168647 + GSM6752680_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552893 + SAMN32855543 + GSM6752680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119205 + + GSM6752679: 4-week HP Grin2a WT snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552891 + GSM6752679 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752679 + + + + + + + GEO Accession + GSM6752679 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552891 + SAMN32855542 + GSM6752679 + + 4-week HP Grin2a WT snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552891 + SAMN32855542 + GSM6752679 + + + + + + + SRR23168644 + GSM6752679_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552891 + SAMN32855542 + GSM6752679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168645 + GSM6752679_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552891 + SAMN32855542 + GSM6752679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119204 + + GSM6752678: 4-week HP Grin2a WT snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552892 + GSM6752678 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752678 + + + + + + + GEO Accession + GSM6752678 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552892 + SAMN32855541 + GSM6752678 + + 4-week HP Grin2a WT snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552892 + SAMN32855541 + GSM6752678 + + + + + + + SRR23168642 + GSM6752678_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552892 + SAMN32855541 + GSM6752678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168643 + GSM6752678_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552892 + SAMN32855541 + GSM6752678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119203 + + GSM6752677: 4-week HP Grin2a WT snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552890 + GSM6752677 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752677 + + + + + + + GEO Accession + GSM6752677 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552890 + SAMN32855540 + GSM6752677 + + 4-week HP Grin2a WT snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + age + 4-week + + + + + + + SRS16552890 + SAMN32855540 + GSM6752677 + + + + + + + SRR23168640 + GSM6752677_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552890 + SAMN32855540 + GSM6752677 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168641 + GSM6752677_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552890 + SAMN32855540 + GSM6752677 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119202 + + GSM6752676: 4-week HP Grin2a -/- snRNA-seq Sample4; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552889 + GSM6752676 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752676 + + + + + + + GEO Accession + GSM6752676 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552889 + SAMN32855539 + GSM6752676 + + 4-week HP Grin2a -/- snRNA-seq Sample4 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552889 + SAMN32855539 + GSM6752676 + + + + + + + SRR23168638 + GSM6752676_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552889 + SAMN32855539 + GSM6752676 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168639 + GSM6752676_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552889 + SAMN32855539 + GSM6752676 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119201 + + GSM6752675: 4-week HP Grin2a -/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552888 + GSM6752675 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752675 + + + + + + + GEO Accession + GSM6752675 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552888 + SAMN32855538 + GSM6752675 + + 4-week HP Grin2a -/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552888 + SAMN32855538 + GSM6752675 + + + + + + + SRR23168636 + GSM6752675_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552888 + SAMN32855538 + GSM6752675 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168637 + GSM6752675_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552888 + SAMN32855538 + GSM6752675 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119200 + + GSM6752674: 4-week HP Grin2a -/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552887 + GSM6752674 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752674 + + + + + + + GEO Accession + GSM6752674 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552887 + SAMN32855537 + GSM6752674 + + 4-week HP Grin2a -/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552887 + SAMN32855537 + GSM6752674 + + + + + + + SRR23168634 + GSM6752674_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552887 + SAMN32855537 + GSM6752674 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168635 + GSM6752674_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552887 + SAMN32855537 + GSM6752674 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119199 + + GSM6752673: 4-week HP Grin2a -/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552884 + GSM6752673 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752673 + + + + + + + GEO Accession + GSM6752673 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552884 + SAMN32855536 + GSM6752673 + + 4-week HP Grin2a -/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a -/- + + + age + 4-week + + + + + + + SRS16552884 + SAMN32855536 + GSM6752673 + + + + + + + SRR23168632 + GSM6752673_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552884 + SAMN32855536 + GSM6752673 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168633 + GSM6752673_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552884 + SAMN32855536 + GSM6752673 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119198 + + GSM6752672: 4-week HP Grin2a +/- snRNA-seq Sample3; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552886 + GSM6752672 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752672 + + + + + + + GEO Accession + GSM6752672 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552886 + SAMN32855535 + GSM6752672 + + 4-week HP Grin2a +/- snRNA-seq Sample3 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552886 + SAMN32855535 + GSM6752672 + + + + + + + SRR23168630 + GSM6752672_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552886 + SAMN32855535 + GSM6752672 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168631 + GSM6752672_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552886 + SAMN32855535 + GSM6752672 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119197 + + GSM6752671: 4-week HP Grin2a +/- snRNA-seq Sample2; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552883 + GSM6752671 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752671 + + + + + + + GEO Accession + GSM6752671 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552883 + SAMN32855534 + GSM6752671 + + 4-week HP Grin2a +/- snRNA-seq Sample2 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552883 + SAMN32855534 + GSM6752671 + + + + + + + SRR23168628 + GSM6752671_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552883 + SAMN32855534 + GSM6752671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168629 + GSM6752671_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552883 + SAMN32855534 + GSM6752671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19119196 + + GSM6752670: 4-week HP Grin2a +/- snRNA-seq Sample1; Mus musculus; RNA-Seq + + + SRP418498 + PRJNA904338 + + + + + + + SRS16552885 + GSM6752670 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe). Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer's protocol. snRNA-seq + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306752670 + + + + + + + GEO Accession + GSM6752670 + + + + + + SRA1577700 + GEO: GSE218572 + + + + NCBI + + + Geo + Curators + + + + + + SRP418498 + PRJNA904338 + GSE218572 + + + Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq] + + To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age. Overall design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice. + GSE218572 + + + + + pubmed + 37657442 + + + + + + parent_bioproject + PRJNA904331 + + + + + + SRS16552885 + SAMN32855533 + GSM6752670 + + 4-week HP Grin2a +/- snRNA-seq Sample1 + + 10090 + Mus musculus + + + + + bioproject + 904338 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Grin2a +/- + + + age + 4-week + + + + + + + SRS16552885 + SAMN32855533 + GSM6752670 + + + + + + + SRR23168626 + GSM6752670_r1 + + + + + loader + fastq-load.py + + + + + + SRS16552885 + SAMN32855533 + GSM6752670 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23168627 + GSM6752670_r2 + + + + + loader + fastq-load.py + + + + + + SRS16552885 + SAMN32855533 + GSM6752670 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE219280.xml b/tests/data/GSE219280.xml new file mode 100644 index 0000000..ab263c4 --- /dev/null +++ b/tests/data/GSE219280.xml @@ -0,0 +1,14522 @@ + + + + + + + SRX18476835 + + GSM6781936: snRNA, Control donor C5, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950536 + GSM6781936 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781936 + + + + + + + GEO Accession + GSM6781936 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + snRNA, Control donor C5, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C5 + + + disease + Control + + + Sex + female + + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + + + + + + SRR22512300 + GSM6781936_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512301 + GSM6781936_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512302 + GSM6781936_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512303 + GSM6781936_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950536 + SAMN32011576 + GSM6781936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476834 + + GSM6781935: snRNA, Control donor C4, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950535 + GSM6781935 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781935 + + + + + + + GEO Accession + GSM6781935 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + snRNA, Control donor C4, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C4 + + + disease + Control + + + Sex + male + + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + + + + + + SRR22512296 + GSM6781935_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512297 + GSM6781935_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512298 + GSM6781935_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512299 + GSM6781935_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950535 + SAMN32011575 + GSM6781935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476833 + + GSM6781934: snRNA, Control donor C4, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950534 + GSM6781934 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781934 + + + + + + + GEO Accession + GSM6781934 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + snRNA, Control donor C4, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C4 + + + disease + Control + + + Sex + male + + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + + + + + + SRR22512292 + GSM6781934_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512293 + GSM6781934_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512294 + GSM6781934_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512295 + GSM6781934_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950534 + SAMN32011574 + GSM6781934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476832 + + GSM6781933: snRNA, Control donor C3, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950533 + GSM6781933 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781933 + + + + + + + GEO Accession + GSM6781933 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + snRNA, Control donor C3, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C3 + + + disease + Control + + + Sex + male + + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + + + + + + SRR22512288 + GSM6781933_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512289 + GSM6781933_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512290 + GSM6781933_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512291 + GSM6781933_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950533 + SAMN32011573 + GSM6781933 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476831 + + GSM6781932: snRNA, Control donor C3, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950532 + GSM6781932 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781932 + + + + + + + GEO Accession + GSM6781932 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + snRNA, Control donor C3, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C3 + + + disease + Control + + + Sex + male + + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + + + + + + SRR22512284 + GSM6781932_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512285 + GSM6781932_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512286 + GSM6781932_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512287 + GSM6781932_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950532 + SAMN32011572 + GSM6781932 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476830 + + GSM6781931: snRNA, Control donor C2, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950531 + GSM6781931 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781931 + + + + + + + GEO Accession + GSM6781931 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + snRNA, Control donor C2, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C2 + + + disease + Control + + + Sex + male + + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + + + + + + SRR22512280 + GSM6781931_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512281 + GSM6781931_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512282 + GSM6781931_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512283 + GSM6781931_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950531 + SAMN32011571 + GSM6781931 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476829 + + GSM6781930: snRNA, Control donor C2, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950530 + GSM6781930 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781930 + + + + + + + GEO Accession + GSM6781930 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + snRNA, Control donor C2, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C2 + + + disease + Control + + + Sex + male + + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + + + + + + SRR22512276 + GSM6781930_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512277 + GSM6781930_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512278 + GSM6781930_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512279 + GSM6781930_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950530 + SAMN32011570 + GSM6781930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476828 + + GSM6781929: snRNA, Control donor C1, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950529 + GSM6781929 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781929 + + + + + + + GEO Accession + GSM6781929 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + snRNA, Control donor C1, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C1 + + + disease + Control + + + Sex + female + + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + + + + + + SRR22512272 + GSM6781929_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512273 + GSM6781929_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512274 + GSM6781929_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512275 + GSM6781929_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950529 + SAMN32011569 + GSM6781929 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476827 + + GSM6781928: snRNA, Control donor C1, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950528 + GSM6781928 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781928 + + + + + + + GEO Accession + GSM6781928 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + snRNA, Control donor C1, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C1 + + + disease + Control + + + Sex + female + + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + + + + + + SRR22512268 + GSM6781928_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512269 + GSM6781928_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512270 + GSM6781928_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512271 + GSM6781928_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950528 + SAMN32011568 + GSM6781928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476826 + + GSM6781927: snRNA, C9-FTD donor F5, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950527 + GSM6781927 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781927 + + + + + + + GEO Accession + GSM6781927 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + snRNA, C9-FTD donor F5, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + F5 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + + + + + + SRR22512264 + GSM6781927_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512265 + GSM6781927_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512266 + GSM6781927_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512267 + GSM6781927_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950527 + SAMN32011567 + GSM6781927 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476825 + + GSM6781926: snRNA, C9-FTD donor F5, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950526 + GSM6781926 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781926 + + + + + + + GEO Accession + GSM6781926 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + snRNA, C9-FTD donor F5, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + F5 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + + + + + + SRR22512260 + GSM6781926_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512261 + GSM6781926_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512262 + GSM6781926_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512263 + GSM6781926_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950526 + SAMN32011566 + GSM6781926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476824 + + GSM6781925: snRNA, C9-FTD donor F4, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950525 + GSM6781925 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781925 + + + + + + + GEO Accession + GSM6781925 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + snRNA, C9-FTD donor F4, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + F4 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + + + + + + SRR22512256 + GSM6781925_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512257 + GSM6781925_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512258 + GSM6781925_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512259 + GSM6781925_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950525 + SAMN32011565 + GSM6781925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476823 + + GSM6781924: snRNA, C9-FTD donor F4, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950524 + GSM6781924 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781924 + + + + + + + GEO Accession + GSM6781924 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + snRNA, C9-FTD donor F4, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + F4 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + + + + + + SRR22512252 + GSM6781924_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512253 + GSM6781924_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512254 + GSM6781924_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512255 + GSM6781924_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950524 + SAMN32011564 + GSM6781924 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476822 + + GSM6781923: snRNA, C9-FTD donor F3, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950523 + GSM6781923 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781923 + + + + + + + GEO Accession + GSM6781923 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + snRNA, C9-FTD donor F3, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + F3 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + + + + + + SRR22512248 + GSM6781923_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512249 + GSM6781923_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512250 + GSM6781923_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512251 + GSM6781923_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950523 + SAMN32011563 + GSM6781923 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476821 + + GSM6781922: snRNA, C9-FTD donor F3, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950522 + GSM6781922 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781922 + + + + + + + GEO Accession + GSM6781922 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + snRNA, C9-FTD donor F3, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + F3 + + + disease + C9-FTD + + + Sex + male + + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + + + + + + SRR22512244 + GSM6781922_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512245 + GSM6781922_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512246 + GSM6781922_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512247 + GSM6781922_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950522 + SAMN32011562 + GSM6781922 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476820 + + GSM6781921: snRNA, C9-FTD donor F2, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950521 + GSM6781921 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781921 + + + + + + + GEO Accession + GSM6781921 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + snRNA, C9-FTD donor F2, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + F2 + + + disease + C9-FTD + + + Sex + female + + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + + + + + + SRR22512240 + GSM6781921_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512241 + GSM6781921_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512242 + GSM6781921_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512243 + GSM6781921_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950521 + SAMN32011561 + GSM6781921 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476819 + + GSM6781920: snRNA, C9-FTD donor F2, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950520 + GSM6781920 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781920 + + + + + + + GEO Accession + GSM6781920 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + snRNA, C9-FTD donor F2, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + F2 + + + disease + C9-FTD + + + Sex + female + + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + + + + + + SRR22512236 + GSM6781920_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512237 + GSM6781920_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512238 + GSM6781920_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512239 + GSM6781920_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950520 + SAMN32011560 + GSM6781920 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476818 + + GSM6781919: snRNA, C9-FTD donor F1, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950519 + GSM6781919 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781919 + + + + + + + GEO Accession + GSM6781919 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + snRNA, C9-FTD donor F1, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + F1 + + + disease + C9-FTD + + + Sex + female + + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + + + + + + SRR22512232 + GSM6781919_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512233 + GSM6781919_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512234 + GSM6781919_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512235 + GSM6781919_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950519 + SAMN32011559 + GSM6781919 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476817 + + GSM6781918: snRNA, C9-FTD donor F1, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950518 + GSM6781918 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781918 + + + + + + + GEO Accession + GSM6781918 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + snRNA, C9-FTD donor F1, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + F1 + + + disease + C9-FTD + + + Sex + female + + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + + + + + + SRR22512228 + GSM6781918_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512229 + GSM6781918_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512230 + GSM6781918_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512231 + GSM6781918_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950518 + SAMN32011558 + GSM6781918 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476816 + + GSM6781917: snRNA, C9-ALS donor A6, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950517 + GSM6781917 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781917 + + + + + + + GEO Accession + GSM6781917 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + snRNA, C9-ALS donor A6, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A6 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + + + + + + SRR22512224 + GSM6781917_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512225 + GSM6781917_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512226 + GSM6781917_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512227 + GSM6781917_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950517 + SAMN32011557 + GSM6781917 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476815 + + GSM6781916: snRNA, C9-ALS donor A6, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950516 + GSM6781916 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781916 + + + + + + + GEO Accession + GSM6781916 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + snRNA, C9-ALS donor A6, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A6 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + + + + + + SRR22512220 + GSM6781916_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512221 + GSM6781916_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512222 + GSM6781916_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512223 + GSM6781916_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950516 + SAMN32011556 + GSM6781916 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476814 + + GSM6781915: snRNA, C9-ALS donor A5, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950515 + GSM6781915 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781915 + + + + + + + GEO Accession + GSM6781915 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + snRNA, C9-ALS donor A5, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A5 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + + + + + + SRR22512216 + GSM6781915_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512217 + GSM6781915_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512218 + GSM6781915_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512219 + GSM6781915_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950515 + SAMN32011555 + GSM6781915 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476813 + + GSM6781914: snRNA, C9-ALS donor A5, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950514 + GSM6781914 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781914 + + + + + + + GEO Accession + GSM6781914 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + snRNA, C9-ALS donor A5, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A5 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + + + + + + SRR22512212 + GSM6781914_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512213 + GSM6781914_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512214 + GSM6781914_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512215 + GSM6781914_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950514 + SAMN32011554 + GSM6781914 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476812 + + GSM6781939: snRNA, Control donor C6, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950513 + GSM6781939 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781939 + + + + + + + GEO Accession + GSM6781939 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + snRNA, Control donor C6, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C6 + + + disease + Control + + + Sex + female + + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + + + + + + SRR22512312 + GSM6781939_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512313 + GSM6781939_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512314 + GSM6781939_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512315 + GSM6781939_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950513 + SAMN32011608 + GSM6781939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476811 + + GSM6781938: snRNA, Control donor C6, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950512 + GSM6781938 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781938 + + + + + + + GEO Accession + GSM6781938 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + snRNA, Control donor C6, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + N/A + + + donor id + C6 + + + disease + Control + + + Sex + female + + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + + + + + + SRR22512308 + GSM6781938_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512309 + GSM6781938_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512310 + GSM6781938_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512311 + GSM6781938_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950512 + SAMN32011607 + GSM6781938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476810 + + GSM6781937: snRNA, Control donor C5, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950511 + GSM6781937 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781937 + + + + + + + GEO Accession + GSM6781937 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + snRNA, Control donor C5, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + N/A + + + donor id + C5 + + + disease + Control + + + Sex + female + + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + + + + + + SRR22512304 + GSM6781937_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512305 + GSM6781937_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512306 + GSM6781937_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512307 + GSM6781937_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950511 + SAMN32011606 + GSM6781937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476809 + + GSM6781913: snRNA, C9-ALS donor A4, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950510 + GSM6781913 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781913 + + + + + + + GEO Accession + GSM6781913 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + snRNA, C9-ALS donor A4, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A4 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + + + + + + SRR22512208 + GSM6781913_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512209 + GSM6781913_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512210 + GSM6781913_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512211 + GSM6781913_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950510 + SAMN32011553 + GSM6781913 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476808 + + GSM6781912: snRNA, C9-ALS donor A4, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950509 + GSM6781912 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781912 + + + + + + + GEO Accession + GSM6781912 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + snRNA, C9-ALS donor A4, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A4 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + + + + + + SRR22512204 + GSM6781912_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512205 + GSM6781912_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512206 + GSM6781912_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512207 + GSM6781912_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950509 + SAMN32011552 + GSM6781912 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476807 + + GSM6781911: snRNA, C9-ALS donor A3, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950508 + GSM6781911 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781911 + + + + + + + GEO Accession + GSM6781911 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + snRNA, C9-ALS donor A3, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A3 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + + + + + + SRR22512200 + GSM6781911_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512201 + GSM6781911_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512202 + GSM6781911_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512203 + GSM6781911_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950508 + SAMN32011551 + GSM6781911 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476806 + + GSM6781910: snRNA, C9-ALS donor A3, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950507 + GSM6781910 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781910 + + + + + + + GEO Accession + GSM6781910 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + snRNA, C9-ALS donor A3, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A3 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + + + + + + SRR22512196 + GSM6781910_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512197 + GSM6781910_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512198 + GSM6781910_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512199 + GSM6781910_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950507 + SAMN32011550 + GSM6781910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476805 + + GSM6781909: snRNA, C9-ALS donor A2, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950506 + GSM6781909 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781909 + + + + + + + GEO Accession + GSM6781909 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + snRNA, C9-ALS donor A2, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A2 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + + + + + + SRR22512192 + GSM6781909_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512193 + GSM6781909_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512194 + GSM6781909_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512195 + GSM6781909_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950506 + SAMN32011549 + GSM6781909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476804 + + GSM6781908: snRNA, C9-ALS donor A2, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950505 + GSM6781908 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781908 + + + + + + + GEO Accession + GSM6781908 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + snRNA, C9-ALS donor A2, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A2 + + + disease + C9-ALS + + + Sex + female + + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + + + + + + SRR22512188 + GSM6781908_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512189 + GSM6781908_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512190 + GSM6781908_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512191 + GSM6781908_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950505 + SAMN32011548 + GSM6781908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476803 + + GSM6781907: snRNA, C9-ALS donor A1, Motor cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950504 + GSM6781907 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781907 + + + + + + + GEO Accession + GSM6781907 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + snRNA, C9-ALS donor A1, Motor cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + motor cortex + + + tissue + motor cortex + + + genotype + C9ORF72+ + + + donor id + A1 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + + + + + + SRR22512184 + GSM6781907_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512185 + GSM6781907_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512186 + GSM6781907_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512187 + GSM6781907_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950504 + SAMN32011547 + GSM6781907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX18476802 + + GSM6781906: snRNA, C9-ALS donor A1, Frontal cortex; Homo sapiens; RNA-Seq + + + SRP411192 + + + + + + + SRS15950503 + GSM6781906 + + + + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407). Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3' system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of ~10,870 unique molecular identifiers (UMIs) per nucleus. + + + + + Illumina NovaSeq 6000 + + + + + + gds + 306781906 + + + + + + + GEO Accession + GSM6781906 + + + + + + SRA1551760 + GEO: GSE219280 + + + + NCBI + + + Geo + Curators + + + + + + SRP411192 + PRJNA907949 + GSE219280 + + + Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq) + + Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes. Overall design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform. + GSE219280 + + + + + pubmed + 37714849 + + + + + + parent_bioproject + PRJNA907856 + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + snRNA, C9-ALS donor A1, Frontal cortex + + 9606 + Homo sapiens + + + + + bioproject + 907949 + + + + + + + source_name + frontal cortex + + + tissue + frontal cortex + + + genotype + C9ORF72+ + + + donor id + A1 + + + disease + C9-ALS + + + Sex + male + + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + + + + + + SRR22512180 + GSM6781906_r1 + + + + + loader + fastq-load.py + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512181 + GSM6781906_r2 + + + + + loader + fastq-load.py + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512182 + GSM6781906_r3 + + + + + loader + fastq-load.py + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR22512183 + GSM6781906_r4 + + + + + loader + fastq-load.py + + + + + + SRS15950503 + SAMN32011595 + GSM6781906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE222510.xml b/tests/data/GSE222510.xml new file mode 100644 index 0000000..d1c4bbe --- /dev/null +++ b/tests/data/GSE222510.xml @@ -0,0 +1,12716 @@ + + + + + + + SRX18986692 + GSM6925176_r1 + + GSM6925176: YY4R: young isochronic parabiont 4 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407757 + GSM6925176 + + + + GSM6925176 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407757 + SAMN32648498 + GSM6925176 + + YY4R: young isochronic parabiont 4 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407757 + SAMN32648498 + GSM6925176 + + + + + + + SRR23031936 + GSM6925176_r1 + + + + GSM6925176_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407757 + SAMN32648498 + GSM6925176 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986691 + GSM6925175_r1 + + GSM6925175: YY4L: young isochronic parabiont 4 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407756 + GSM6925175 + + + + GSM6925175 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407756 + SAMN32648499 + GSM6925175 + + YY4L: young isochronic parabiont 4 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407756 + SAMN32648499 + GSM6925175 + + + + + + + SRR23031937 + GSM6925175_r1 + + + + GSM6925175_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407756 + SAMN32648499 + GSM6925175 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986690 + GSM6925174_r1 + + GSM6925174: YY3R: young isochronic parabiont 3 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407755 + GSM6925174 + + + + GSM6925174 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407755 + SAMN32648500 + GSM6925174 + + YY3R: young isochronic parabiont 3 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407755 + SAMN32648500 + GSM6925174 + + + + + + + SRR23031938 + GSM6925174_r1 + + + + GSM6925174_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407755 + SAMN32648500 + GSM6925174 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986689 + GSM6925173_r1 + + GSM6925173: YY3L: young isochronic parabiont 3 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407754 + GSM6925173 + + + + GSM6925173 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407754 + SAMN32648501 + GSM6925173 + + YY3L: young isochronic parabiont 3 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407754 + SAMN32648501 + GSM6925173 + + + + + + + SRR23031939 + GSM6925173_r1 + + + + GSM6925173_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407754 + SAMN32648501 + GSM6925173 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986688 + GSM6925172_r1 + + GSM6925172: YY2R: young isocrhonic parabiont 2 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407753 + GSM6925172 + + + + GSM6925172 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407753 + SAMN32648502 + GSM6925172 + + YY2R: young isocrhonic parabiont 2 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407753 + SAMN32648502 + GSM6925172 + + + + + + + SRR23031940 + GSM6925172_r1 + + + + GSM6925172_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407753 + SAMN32648502 + GSM6925172 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986687 + GSM6925171_r1 + + GSM6925171: YY2L: young isochronic parabiont 2 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407752 + GSM6925171 + + + + GSM6925171 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407752 + SAMN32648503 + GSM6925171 + + YY2L: young isochronic parabiont 2 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407752 + SAMN32648503 + GSM6925171 + + + + + + + SRR23031941 + GSM6925171_r1 + + + + GSM6925171_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407752 + SAMN32648503 + GSM6925171 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986686 + GSM6925170_r1 + + GSM6925170: YY1R: young isochronic parabiont 1 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407751 + GSM6925170 + + + + GSM6925170 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + YY1R: young isochronic parabiont 1 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + + + + + + SRR23031942 + GSM6925170_r1 + + + + GSM6925170_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986685 + GSM6925169_r1 + + GSM6925169: YY1L: young isochronic parabiont 1 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407750 + GSM6925169 + + + + GSM6925169 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407750 + SAMN32648505 + GSM6925169 + + YY1L: young isochronic parabiont 1 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407750 + SAMN32648505 + GSM6925169 + + + + + + + SRR23031943 + GSM6925169_r1 + + + + GSM6925169_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407750 + SAMN32648505 + GSM6925169 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986684 + GSM6925168_r1 + + GSM6925168: YX8L: young animal 8; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407749 + GSM6925168 + + + + GSM6925168 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407749 + SAMN32648506 + GSM6925168 + + YX8L: young animal 8 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407749 + SAMN32648506 + GSM6925168 + + + + + + + SRR23031944 + GSM6925168_r1 + + + + GSM6925168_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407749 + SAMN32648506 + GSM6925168 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986683 + GSM6925167_r1 + + GSM6925167: YX7R: young animal 7; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407748 + GSM6925167 + + + + GSM6925167 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407748 + SAMN32648507 + GSM6925167 + + YX7R: young animal 7 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407748 + SAMN32648507 + GSM6925167 + + + + + + + SRR23031945 + GSM6925167_r1 + + + + GSM6925167_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407748 + SAMN32648507 + GSM6925167 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986682 + GSM6925166_r1 + + GSM6925166: YX6L: young animal 6; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407747 + GSM6925166 + + + + GSM6925166 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407747 + SAMN32648508 + GSM6925166 + + YX6L: young animal 6 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407747 + SAMN32648508 + GSM6925166 + + + + + + + SRR23031946 + GSM6925166_r1 + + + + GSM6925166_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407747 + SAMN32648508 + GSM6925166 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986681 + GSM6925165_r1 + + GSM6925165: YX5R: young animal 5; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407746 + GSM6925165 + + + + GSM6925165 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407746 + SAMN32648509 + GSM6925165 + + YX5R: young animal 5 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407746 + SAMN32648509 + GSM6925165 + + + + + + + SRR23031947 + GSM6925165_r1 + + + + GSM6925165_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407746 + SAMN32648509 + GSM6925165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986680 + GSM6925164_r1 + + GSM6925164: YX4R: young animal 4; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407745 + GSM6925164 + + + + GSM6925164 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407745 + SAMN32648510 + GSM6925164 + + YX4R: young animal 4 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407745 + SAMN32648510 + GSM6925164 + + + + + + + SRR23031948 + GSM6925164_r1 + + + + GSM6925164_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407745 + SAMN32648510 + GSM6925164 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986679 + GSM6925163_r1 + + GSM6925163: YX3R: young animal 3; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407744 + GSM6925163 + + + + GSM6925163 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407744 + SAMN32648511 + GSM6925163 + + YX3R: young animal 3 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407744 + SAMN32648511 + GSM6925163 + + + + + + + SRR23031949 + GSM6925163_r1 + + + + GSM6925163_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407744 + SAMN32648511 + GSM6925163 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986678 + GSM6925162_r1 + + GSM6925162: YX2L: young animal 2; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407743 + GSM6925162 + + + + GSM6925162 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407743 + SAMN32648512 + GSM6925162 + + YX2L: young animal 2 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407743 + SAMN32648512 + GSM6925162 + + + + + + + SRR23031950 + GSM6925162_r1 + + + + GSM6925162_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407743 + SAMN32648512 + GSM6925162 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986677 + GSM6925161_r1 + + GSM6925161: YX1L: young animal 1; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407742 + GSM6925161 + + + + GSM6925161 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407742 + SAMN32648513 + GSM6925161 + + YX1L: young animal 1 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 2-3 months old + + + treatment + unpaired + + + + + + + SRS16407742 + SAMN32648513 + GSM6925161 + + + + + + + SRR23031951 + GSM6925161_r1 + + + + GSM6925161_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407742 + SAMN32648513 + GSM6925161 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986676 + GSM6925160_r1 + + GSM6925160: YO9X: young heterochronic parabiont 9; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407741 + GSM6925160 + + + + GSM6925160 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407741 + SAMN32648514 + GSM6925160 + + YO9X: young heterochronic parabiont 9 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407741 + SAMN32648514 + GSM6925160 + + + + + + + SRR23031952 + GSM6925160_r1 + + + + GSM6925160_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407741 + SAMN32648514 + GSM6925160 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986675 + GSM6925159_r1 + + GSM6925159: YO8X: young heterochronic parabiont 8; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407740 + GSM6925159 + + + + GSM6925159 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407740 + SAMN32648515 + GSM6925159 + + YO8X: young heterochronic parabiont 8 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407740 + SAMN32648515 + GSM6925159 + + + + + + + SRR23031953 + GSM6925159_r1 + + + + GSM6925159_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407740 + SAMN32648515 + GSM6925159 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986674 + GSM6925158_r1 + + GSM6925158: YO7X: young heterochronic parabiont 7; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407739 + GSM6925158 + + + + GSM6925158 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407739 + SAMN32648516 + GSM6925158 + + YO7X: young heterochronic parabiont 7 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407739 + SAMN32648516 + GSM6925158 + + + + + + + SRR23031954 + GSM6925158_r1 + + + + GSM6925158_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407739 + SAMN32648516 + GSM6925158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986673 + GSM6925157_r1 + + GSM6925157: YO6X: young heterochronic parabiont 6; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407738 + GSM6925157 + + + + GSM6925157 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407738 + SAMN32648517 + GSM6925157 + + YO6X: young heterochronic parabiont 6 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407738 + SAMN32648517 + GSM6925157 + + + + + + + SRR23031955 + GSM6925157_r1 + + + + GSM6925157_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407738 + SAMN32648517 + GSM6925157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986672 + GSM6925156_r1 + + GSM6925156: YO5X: young heterochronic parabiont 5; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407737 + GSM6925156 + + + + GSM6925156 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407737 + SAMN32648518 + GSM6925156 + + YO5X: young heterochronic parabiont 5 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407737 + SAMN32648518 + GSM6925156 + + + + + + + SRR23031956 + GSM6925156_r1 + + + + GSM6925156_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407737 + SAMN32648518 + GSM6925156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986671 + GSM6925155_r1 + + GSM6925155: YO4X: young heterochronic parabiont 4; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407736 + GSM6925155 + + + + GSM6925155 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407736 + SAMN32648519 + GSM6925155 + + YO4X: young heterochronic parabiont 4 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407736 + SAMN32648519 + GSM6925155 + + + + + + + SRR23031957 + GSM6925155_r1 + + + + GSM6925155_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407736 + SAMN32648519 + GSM6925155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986670 + GSM6925154_r1 + + GSM6925154: YO3X: young heterochronic parabiont 3; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407735 + GSM6925154 + + + + GSM6925154 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407735 + SAMN32648520 + GSM6925154 + + YO3X: young heterochronic parabiont 3 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407735 + SAMN32648520 + GSM6925154 + + + + + + + SRR23031958 + GSM6925154_r1 + + + + GSM6925154_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407735 + SAMN32648520 + GSM6925154 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986669 + GSM6925153_r1 + + GSM6925153: YO2X: young heterochronic parabiont 2; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407734 + GSM6925153 + + + + GSM6925153 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407734 + SAMN32648521 + GSM6925153 + + YO2X: young heterochronic parabiont 2 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407734 + SAMN32648521 + GSM6925153 + + + + + + + SRR23031959 + GSM6925153_r1 + + + + GSM6925153_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407734 + SAMN32648521 + GSM6925153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986668 + GSM6925152_r1 + + GSM6925152: YO1X: young heterochronic parabiont 1; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407733 + GSM6925152 + + + + GSM6925152 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407733 + SAMN32648522 + GSM6925152 + + YO1X: young heterochronic parabiont 1 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407733 + SAMN32648522 + GSM6925152 + + + + + + + SRR23031960 + GSM6925152_r1 + + + + GSM6925152_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407733 + SAMN32648522 + GSM6925152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986667 + GSM6925151_r1 + + GSM6925151: OY11X: old heterochronic parabiont 11; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407732 + GSM6925151 + + + + GSM6925151 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407732 + SAMN32648523 + GSM6925151 + + OY11X: old heterochronic parabiont 11 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407732 + SAMN32648523 + GSM6925151 + + + + + + + SRR23031961 + GSM6925151_r1 + + + + GSM6925151_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407732 + SAMN32648523 + GSM6925151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986666 + GSM6925150_r1 + + GSM6925150: OY10X: old heterochronic parabiont 10; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407731 + GSM6925150 + + + + GSM6925150 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407731 + SAMN32648524 + GSM6925150 + + OY10X: old heterochronic parabiont 10 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407731 + SAMN32648524 + GSM6925150 + + + + + + + SRR23031962 + GSM6925150_r1 + + + + GSM6925150_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407731 + SAMN32648524 + GSM6925150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986665 + GSM6925149_r1 + + GSM6925149: OY9X: old heterochronic parabiont 9; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407730 + GSM6925149 + + + + GSM6925149 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407730 + SAMN32648525 + GSM6925149 + + OY9X: old heterochronic parabiont 9 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407730 + SAMN32648525 + GSM6925149 + + + + + + + SRR23031963 + GSM6925149_r1 + + + + GSM6925149_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407730 + SAMN32648525 + GSM6925149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986664 + GSM6925148_r1 + + GSM6925148: OY8X: old heterochronic parabiont 8; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407729 + GSM6925148 + + + + GSM6925148 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407729 + SAMN32648526 + GSM6925148 + + OY8X: old heterochronic parabiont 8 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407729 + SAMN32648526 + GSM6925148 + + + + + + + SRR23031964 + GSM6925148_r1 + + + + GSM6925148_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407729 + SAMN32648526 + GSM6925148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986663 + GSM6925147_r1 + + GSM6925147: OY7X: old heterochronic parabiont 7; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407728 + GSM6925147 + + + + GSM6925147 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407728 + SAMN32648527 + GSM6925147 + + OY7X: old heterochronic parabiont 7 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407728 + SAMN32648527 + GSM6925147 + + + + + + + SRR23031965 + GSM6925147_r1 + + + + GSM6925147_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407728 + SAMN32648527 + GSM6925147 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986662 + GSM6925146_r1 + + GSM6925146: OY6X: old heterochronic parabiont 6; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407727 + GSM6925146 + + + + GSM6925146 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407727 + SAMN32648528 + GSM6925146 + + OY6X: old heterochronic parabiont 6 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407727 + SAMN32648528 + GSM6925146 + + + + + + + SRR23031966 + GSM6925146_r1 + + + + GSM6925146_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407727 + SAMN32648528 + GSM6925146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986661 + GSM6925145_r1 + + GSM6925145: OY5X: old heterochronic parabiont 5; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407726 + GSM6925145 + + + + GSM6925145 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407726 + SAMN32648529 + GSM6925145 + + OY5X: old heterochronic parabiont 5 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407726 + SAMN32648529 + GSM6925145 + + + + + + + SRR23031967 + GSM6925145_r1 + + + + GSM6925145_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407726 + SAMN32648529 + GSM6925145 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986660 + GSM6925144_r1 + + GSM6925144: OY4X: old heterochronic parabiont 4; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407725 + GSM6925144 + + + + GSM6925144 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407725 + SAMN32648530 + GSM6925144 + + OY4X: old heterochronic parabiont 4 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407725 + SAMN32648530 + GSM6925144 + + + + + + + SRR23031968 + GSM6925144_r1 + + + + GSM6925144_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407725 + SAMN32648530 + GSM6925144 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986659 + GSM6925143_r1 + + GSM6925143: OY3X: old heterochronic parabiont 3; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407724 + GSM6925143 + + + + GSM6925143 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407724 + SAMN32648531 + GSM6925143 + + OY3X: old heterochronic parabiont 3 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407724 + SAMN32648531 + GSM6925143 + + + + + + + SRR23031969 + GSM6925143_r1 + + + + GSM6925143_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407724 + SAMN32648531 + GSM6925143 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986658 + GSM6925142_r1 + + GSM6925142: OY2X: old heterochronic parabiont 2; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407723 + GSM6925142 + + + + GSM6925142 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407723 + SAMN32648532 + GSM6925142 + + OY2X: old heterochronic parabiont 2 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407723 + SAMN32648532 + GSM6925142 + + + + + + + SRR23031970 + GSM6925142_r1 + + + + GSM6925142_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407723 + SAMN32648532 + GSM6925142 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986657 + GSM6925141_r1 + + GSM6925141: OY1X: old heterochronic parabiont 1; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407722 + GSM6925141 + + + + GSM6925141 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407722 + SAMN32648533 + GSM6925141 + + OY1X: old heterochronic parabiont 1 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + heterochronic parabiosis + + + + + + + SRS16407722 + SAMN32648533 + GSM6925141 + + + + + + + SRR23031971 + GSM6925141_r1 + + + + GSM6925141_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407722 + SAMN32648533 + GSM6925141 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986656 + GSM6925140_r1 + + GSM6925140: OX8X: old animal 8; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407721 + GSM6925140 + + + + GSM6925140 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407721 + SAMN32648534 + GSM6925140 + + OX8X: old animal 8 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407721 + SAMN32648534 + GSM6925140 + + + + + + + SRR23031972 + GSM6925140_r1 + + + + GSM6925140_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407721 + SAMN32648534 + GSM6925140 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986655 + GSM6925139_r1 + + GSM6925139: OX7X: old animal 7; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407720 + GSM6925139 + + + + GSM6925139 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407720 + SAMN32648535 + GSM6925139 + + OX7X: old animal 7 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407720 + SAMN32648535 + GSM6925139 + + + + + + + SRR23031973 + GSM6925139_r1 + + + + GSM6925139_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407720 + SAMN32648535 + GSM6925139 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986654 + GSM6925138_r1 + + GSM6925138: OX6X: old animal 6; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407719 + GSM6925138 + + + + GSM6925138 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407719 + SAMN32648536 + GSM6925138 + + OX6X: old animal 6 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407719 + SAMN32648536 + GSM6925138 + + + + + + + SRR23031974 + GSM6925138_r1 + + + + GSM6925138_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407719 + SAMN32648536 + GSM6925138 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986653 + GSM6925137_r1 + + GSM6925137: OX5X: old animal 5; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407718 + GSM6925137 + + + + GSM6925137 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407718 + SAMN32648537 + GSM6925137 + + OX5X: old animal 5 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407718 + SAMN32648537 + GSM6925137 + + + + + + + SRR23031975 + GSM6925137_r1 + + + + GSM6925137_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407718 + SAMN32648537 + GSM6925137 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986652 + GSM6925136_r1 + + GSM6925136: OX4X: old animal 4; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407717 + GSM6925136 + + + + GSM6925136 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407717 + SAMN32648538 + GSM6925136 + + OX4X: old animal 4 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407717 + SAMN32648538 + GSM6925136 + + + + + + + SRR23031976 + GSM6925136_r1 + + + + GSM6925136_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407717 + SAMN32648538 + GSM6925136 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986651 + GSM6925135_r1 + + GSM6925135: OX3X: old animal 3; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407716 + GSM6925135 + + + + GSM6925135 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407716 + SAMN32648539 + GSM6925135 + + OX3X: old animal 3 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407716 + SAMN32648539 + GSM6925135 + + + + + + + SRR23031977 + GSM6925135_r1 + + + + GSM6925135_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407716 + SAMN32648539 + GSM6925135 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986650 + GSM6925134_r1 + + GSM6925134: OX2X: old animal 2; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407715 + GSM6925134 + + + + GSM6925134 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407715 + SAMN32648540 + GSM6925134 + + OX2X: old animal 2 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407715 + SAMN32648540 + GSM6925134 + + + + + + + SRR23031978 + GSM6925134_r1 + + + + GSM6925134_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407715 + SAMN32648540 + GSM6925134 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986649 + GSM6925133_r1 + + GSM6925133: OX1X: old animal 1; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407714 + GSM6925133 + + + + GSM6925133 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407714 + SAMN32648541 + GSM6925133 + + OX1X: old animal 1 + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 21-22months old + + + treatment + unpaired + + + + + + + SRS16407714 + SAMN32648541 + GSM6925133 + + + + + + + SRR23031979 + GSM6925133_r1 + + + + GSM6925133_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407714 + SAMN32648541 + GSM6925133 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986648 + GSM6925132_r1 + + GSM6925132: OO6R: old isochronic parabiont 6 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407713 + GSM6925132 + + + + GSM6925132 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407713 + SAMN32648542 + GSM6925132 + + OO6R: old isochronic parabiont 6 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407713 + SAMN32648542 + GSM6925132 + + + + + + + SRR23031980 + GSM6925132_r1 + + + + GSM6925132_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407713 + SAMN32648542 + GSM6925132 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986647 + GSM6925131_r1 + + GSM6925131: OO6L: old isochconic parabiont 6 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407712 + GSM6925131 + + + + GSM6925131 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407712 + SAMN32648543 + GSM6925131 + + OO6L: old isochconic parabiont 6 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407712 + SAMN32648543 + GSM6925131 + + + + + + + SRR23031981 + GSM6925131_r1 + + + + GSM6925131_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407712 + SAMN32648543 + GSM6925131 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986646 + GSM6925130_r1 + + GSM6925130: OO5R: old isocrhonic parabiont 5 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407711 + GSM6925130 + + + + GSM6925130 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407711 + SAMN32648544 + GSM6925130 + + OO5R: old isocrhonic parabiont 5 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407711 + SAMN32648544 + GSM6925130 + + + + + + + SRR23031982 + GSM6925130_r1 + + + + GSM6925130_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407711 + SAMN32648544 + GSM6925130 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986645 + GSM6925129_r1 + + GSM6925129: OO5L: old isochronic parabiont 5 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407710 + GSM6925129 + + + + GSM6925129 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407710 + SAMN32648545 + GSM6925129 + + OO5L: old isochronic parabiont 5 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407710 + SAMN32648545 + GSM6925129 + + + + + + + SRR23031983 + GSM6925129_r1 + + + + GSM6925129_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407710 + SAMN32648545 + GSM6925129 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986644 + GSM6925128_r1 + + GSM6925128: OO4R: old isochronic parabiont 4 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407709 + GSM6925128 + + + + GSM6925128 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407709 + SAMN32648546 + GSM6925128 + + OO4R: old isochronic parabiont 4 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407709 + SAMN32648546 + GSM6925128 + + + + + + + SRR23031984 + GSM6925128_r1 + + + + GSM6925128_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407709 + SAMN32648546 + GSM6925128 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986643 + GSM6925127_r1 + + GSM6925127: OO4L: old isochronic parabiont 4 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407708 + GSM6925127 + + + + GSM6925127 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407708 + SAMN32648547 + GSM6925127 + + OO4L: old isochronic parabiont 4 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407708 + SAMN32648547 + GSM6925127 + + + + + + + SRR23031985 + GSM6925127_r1 + + + + GSM6925127_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407708 + SAMN32648547 + GSM6925127 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986642 + GSM6925126_r1 + + GSM6925126: OO3R: old isochronic parabiont 3 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407707 + GSM6925126 + + + + GSM6925126 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407707 + SAMN32648548 + GSM6925126 + + OO3R: old isochronic parabiont 3 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407707 + SAMN32648548 + GSM6925126 + + + + + + + SRR23031986 + GSM6925126_r1 + + + + GSM6925126_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407707 + SAMN32648548 + GSM6925126 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986641 + GSM6925125_r1 + + GSM6925125: OO3L: old isochronic parabiont 3 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407706 + GSM6925125 + + + + GSM6925125 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407706 + SAMN32648549 + GSM6925125 + + OO3L: old isochronic parabiont 3 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407706 + SAMN32648549 + GSM6925125 + + + + + + + SRR23031987 + GSM6925125_r1 + + + + GSM6925125_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407706 + SAMN32648549 + GSM6925125 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986640 + GSM6925124_r1 + + GSM6925124: OO2R: old isochronic parabiont 2 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407705 + GSM6925124 + + + + GSM6925124 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407705 + SAMN32648550 + GSM6925124 + + OO2R: old isochronic parabiont 2 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407705 + SAMN32648550 + GSM6925124 + + + + + + + SRR23031988 + GSM6925124_r1 + + + + GSM6925124_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407705 + SAMN32648550 + GSM6925124 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986639 + GSM6925123_r1 + + GSM6925123: OO2L: old isochronic parabiont 2 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407704 + GSM6925123 + + + + GSM6925123 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407704 + SAMN32648551 + GSM6925123 + + OO2L: old isochronic parabiont 2 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407704 + SAMN32648551 + GSM6925123 + + + + + + + SRR23031989 + GSM6925123_r1 + + + + GSM6925123_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407704 + SAMN32648551 + GSM6925123 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986638 + GSM6925122_r1 + + GSM6925122: OO1R: old isochronic parabiont 1 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407703 + GSM6925122 + + + + GSM6925122 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407703 + SAMN32648552 + GSM6925122 + + OO1R: old isochronic parabiont 1 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407703 + SAMN32648552 + GSM6925122 + + + + + + + SRR23031990 + GSM6925122_r1 + + + + GSM6925122_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407703 + SAMN32648552 + GSM6925122 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX18986637 + GSM6925121_r1 + + GSM6925121: OO1L: old isochronic parabiont 1 left; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407702 + GSM6925121 + + + + GSM6925121 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407702 + SAMN32648553 + GSM6925121 + + OO1L: old isochronic parabiont 1 left + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 20-22 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407702 + SAMN32648553 + GSM6925121 + + + + + + + SRR23031991 + GSM6925121_r1 + + + + GSM6925121_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407702 + SAMN32648553 + GSM6925121 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE222647.xml b/tests/data/GSE222647.xml new file mode 100644 index 0000000..eaa3f14 --- /dev/null +++ b/tests/data/GSE222647.xml @@ -0,0 +1,15034 @@ + + + + + + + SRX19005568 + GSM6928320_r1 + + GSM6928320: R076, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425480 + GSM6928320 + + + + GSM6928320 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425480 + SAMN32679322 + GSM6928320 + + R076, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425480 + SAMN32679322 + GSM6928320 + + + + + + + SRR23052072 + GSM6928320_r1 + + + + GSM6928320_r1 + + + + + + SRS16425480 + SAMN32679322 + GSM6928320 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005567 + GSM6928319_r1 + + GSM6928319: R074, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425479 + GSM6928319 + + + + GSM6928319 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425479 + SAMN32679323 + GSM6928319 + + R074, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425479 + SAMN32679323 + GSM6928319 + + + + + + + SRR23052073 + GSM6928319_r1 + + + + GSM6928319_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425479 + SAMN32679323 + GSM6928319 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052074 + GSM6928319_r2 + + + + GSM6928319_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425479 + SAMN32679323 + GSM6928319 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005566 + GSM6928318_r1 + + GSM6928318: R073, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425477 + GSM6928318 + + + + GSM6928318 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425477 + SAMN32679324 + GSM6928318 + + R073, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425477 + SAMN32679324 + GSM6928318 + + + + + + + SRR23052075 + GSM6928318_r1 + + + + GSM6928318_r1 + + + + + + SRS16425477 + SAMN32679324 + GSM6928318 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005565 + GSM6928317_r1 + + GSM6928317: R072, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425478 + GSM6928317 + + + + GSM6928317 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425478 + SAMN32679325 + GSM6928317 + + R072, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425478 + SAMN32679325 + GSM6928317 + + + + + + + SRR23052076 + GSM6928317_r1 + + + + GSM6928317_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425478 + SAMN32679325 + GSM6928317 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005564 + GSM6928316_r1 + + GSM6928316: R070, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425476 + GSM6928316 + + + + GSM6928316 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425476 + SAMN32679326 + GSM6928316 + + R070, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425476 + SAMN32679326 + GSM6928316 + + + + + + + SRR23052077 + GSM6928316_r1 + + + + GSM6928316_r1 + + + + + + SRS16425476 + SAMN32679326 + GSM6928316 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005563 + GSM6928315_r1 + + GSM6928315: R069, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425475 + GSM6928315 + + + + GSM6928315 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425475 + SAMN32679327 + GSM6928315 + + R069, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425475 + SAMN32679327 + GSM6928315 + + + + + + + SRR23052078 + GSM6928315_r1 + + + + GSM6928315_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425475 + SAMN32679327 + GSM6928315 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052079 + GSM6928315_r2 + + + + GSM6928315_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425475 + SAMN32679327 + GSM6928315 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005562 + GSM6928314_r1 + + GSM6928314: R068, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425474 + GSM6928314 + + + + GSM6928314 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425474 + SAMN32679328 + GSM6928314 + + R068, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425474 + SAMN32679328 + GSM6928314 + + + + + + + SRR23052080 + GSM6928314_r1 + + + + GSM6928314_r1 + + + + + + SRS16425474 + SAMN32679328 + GSM6928314 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005561 + GSM6928313_r1 + + GSM6928313: R067, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425473 + GSM6928313 + + + + GSM6928313 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425473 + SAMN32679329 + GSM6928313 + + R067, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425473 + SAMN32679329 + GSM6928313 + + + + + + + SRR23052081 + GSM6928313_r1 + + + + GSM6928313_r1 + + + + + + SRS16425473 + SAMN32679329 + GSM6928313 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005560 + GSM6928312_r1 + + GSM6928312: R066, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425472 + GSM6928312 + + + + GSM6928312 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425472 + SAMN32679330 + GSM6928312 + + R066, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425472 + SAMN32679330 + GSM6928312 + + + + + + + SRR23052082 + GSM6928312_r1 + + + + GSM6928312_r1 + + + + + + SRS16425472 + SAMN32679330 + GSM6928312 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005559 + GSM6928311_r1 + + GSM6928311: R065, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425471 + GSM6928311 + + + + GSM6928311 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425471 + SAMN32679331 + GSM6928311 + + R065, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425471 + SAMN32679331 + GSM6928311 + + + + + + + SRR23052083 + GSM6928311_r1 + + + + GSM6928311_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425471 + SAMN32679331 + GSM6928311 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052084 + GSM6928311_r2 + + + + GSM6928311_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425471 + SAMN32679331 + GSM6928311 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005558 + GSM6928310_r1 + + GSM6928310: R064, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425470 + GSM6928310 + + + + GSM6928310 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425470 + SAMN32679332 + GSM6928310 + + R064, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425470 + SAMN32679332 + GSM6928310 + + + + + + + SRR23052085 + GSM6928310_r1 + + + + GSM6928310_r1 + + + + + + SRS16425470 + SAMN32679332 + GSM6928310 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005557 + GSM6928309_r1 + + GSM6928309: R063, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425469 + GSM6928309 + + + + GSM6928309 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425469 + SAMN32679333 + GSM6928309 + + R063, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425469 + SAMN32679333 + GSM6928309 + + + + + + + SRR23052086 + GSM6928309_r1 + + + + GSM6928309_r1 + + + + + + SRS16425469 + SAMN32679333 + GSM6928309 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005556 + GSM6928308_r1 + + GSM6928308: R062, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425468 + GSM6928308 + + + + GSM6928308 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425468 + SAMN32679334 + GSM6928308 + + R062, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425468 + SAMN32679334 + GSM6928308 + + + + + + + SRR23052087 + GSM6928308_r1 + + + + GSM6928308_r1 + + + + + + SRS16425468 + SAMN32679334 + GSM6928308 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005555 + GSM6928307_r1 + + GSM6928307: R061, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425467 + GSM6928307 + + + + GSM6928307 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425467 + SAMN32679335 + GSM6928307 + + R061, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425467 + SAMN32679335 + GSM6928307 + + + + + + + SRR23052088 + GSM6928307_r1 + + + + GSM6928307_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425467 + SAMN32679335 + GSM6928307 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052089 + GSM6928307_r2 + + + + GSM6928307_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425467 + SAMN32679335 + GSM6928307 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005554 + GSM6928306_r1 + + GSM6928306: R060, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425466 + GSM6928306 + + + + GSM6928306 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425466 + SAMN32679336 + GSM6928306 + + R060, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425466 + SAMN32679336 + GSM6928306 + + + + + + + SRR23052090 + GSM6928306_r1 + + + + GSM6928306_r1 + + + + + + SRS16425466 + SAMN32679336 + GSM6928306 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005553 + GSM6928305_r1 + + GSM6928305: R059, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425465 + GSM6928305 + + + + GSM6928305 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425465 + SAMN32679337 + GSM6928305 + + R059, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425465 + SAMN32679337 + GSM6928305 + + + + + + + SRR23052091 + GSM6928305_r1 + + + + GSM6928305_r1 + + + + + + SRS16425465 + SAMN32679337 + GSM6928305 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005552 + GSM6928304_r1 + + GSM6928304: R057, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425464 + GSM6928304 + + + + GSM6928304 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425464 + SAMN32679338 + GSM6928304 + + R057, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425464 + SAMN32679338 + GSM6928304 + + + + + + + SRR23052092 + GSM6928304_r1 + + + + GSM6928304_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425464 + SAMN32679338 + GSM6928304 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052093 + GSM6928304_r2 + + + + GSM6928304_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425464 + SAMN32679338 + GSM6928304 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005551 + GSM6928303_r1 + + GSM6928303: R056, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425463 + GSM6928303 + + + + GSM6928303 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425463 + SAMN32679339 + GSM6928303 + + R056, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425463 + SAMN32679339 + GSM6928303 + + + + + + + SRR23052094 + GSM6928303_r1 + + + + GSM6928303_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425463 + SAMN32679339 + GSM6928303 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052095 + GSM6928303_r2 + + + + GSM6928303_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425463 + SAMN32679339 + GSM6928303 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005550 + GSM6928302_r1 + + GSM6928302: R055, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425461 + GSM6928302 + + + + GSM6928302 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425461 + SAMN32679340 + GSM6928302 + + R055, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425461 + SAMN32679340 + GSM6928302 + + + + + + + SRR23052096 + GSM6928302_r1 + + + + GSM6928302_r1 + + + + + + SRS16425461 + SAMN32679340 + GSM6928302 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005549 + GSM6928301_r1 + + GSM6928301: R054, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425462 + GSM6928301 + + + + GSM6928301 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425462 + SAMN32679341 + GSM6928301 + + R054, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425462 + SAMN32679341 + GSM6928301 + + + + + + + SRR23052097 + GSM6928301_r1 + + + + GSM6928301_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425462 + SAMN32679341 + GSM6928301 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052098 + GSM6928301_r2 + + + + GSM6928301_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425462 + SAMN32679341 + GSM6928301 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005548 + GSM6928299_r1 + + GSM6928299: R052, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425460 + GSM6928299 + + + + GSM6928299 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425460 + SAMN32679343 + GSM6928299 + + R052, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425460 + SAMN32679343 + GSM6928299 + + + + + + + SRR23052099 + GSM6928299_r1 + + + + GSM6928299_r1 + + + + + + SRS16425460 + SAMN32679343 + GSM6928299 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005547 + GSM6928321_r1 + + GSM6928321: R077, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425459 + GSM6928321 + + + + GSM6928321 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425459 + SAMN32679321 + GSM6928321 + + R077, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425459 + SAMN32679321 + GSM6928321 + + + + + + + SRR23052100 + GSM6928321_r1 + + + + GSM6928321_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425459 + SAMN32679321 + GSM6928321 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052101 + GSM6928321_r2 + + + + GSM6928321_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425459 + SAMN32679321 + GSM6928321 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005546 + GSM6928300_r1 + + GSM6928300: R053, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425458 + GSM6928300 + + + + GSM6928300 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425458 + SAMN32679342 + GSM6928300 + + R053, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425458 + SAMN32679342 + GSM6928300 + + + + + + + SRR23052102 + GSM6928300_r1 + + + + GSM6928300_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425458 + SAMN32679342 + GSM6928300 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052103 + GSM6928300_r2 + + + + GSM6928300_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425458 + SAMN32679342 + GSM6928300 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005545 + GSM6928298_r1 + + GSM6928298: R051, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425457 + GSM6928298 + + + + GSM6928298 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425457 + SAMN32679344 + GSM6928298 + + R051, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425457 + SAMN32679344 + GSM6928298 + + + + + + + SRR23052104 + GSM6928298_r1 + + + + GSM6928298_r1 + + + + + + SRS16425457 + SAMN32679344 + GSM6928298 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005544 + GSM6928297_r1 + + GSM6928297: R050, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425456 + GSM6928297 + + + + GSM6928297 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425456 + SAMN32679345 + GSM6928297 + + R050, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425456 + SAMN32679345 + GSM6928297 + + + + + + + SRR23052105 + GSM6928297_r1 + + + + GSM6928297_r1 + + + + + + SRS16425456 + SAMN32679345 + GSM6928297 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005543 + GSM6928296_r1 + + GSM6928296: R049, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425455 + GSM6928296 + + + + GSM6928296 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425455 + SAMN32679346 + GSM6928296 + + R049, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425455 + SAMN32679346 + GSM6928296 + + + + + + + SRR23052106 + GSM6928296_r1 + + + + GSM6928296_r1 + + + + + + SRS16425455 + SAMN32679346 + GSM6928296 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005542 + GSM6928295_r1 + + GSM6928295: R048, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425454 + GSM6928295 + + + + GSM6928295 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425454 + SAMN32679347 + GSM6928295 + + R048, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425454 + SAMN32679347 + GSM6928295 + + + + + + + SRR23052107 + GSM6928295_r1 + + + + GSM6928295_r1 + + + + + + SRS16425454 + SAMN32679347 + GSM6928295 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005541 + GSM6928294_r1 + + GSM6928294: R047, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425453 + GSM6928294 + + + + GSM6928294 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425453 + SAMN32679348 + GSM6928294 + + R047, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425453 + SAMN32679348 + GSM6928294 + + + + + + + SRR23052108 + GSM6928294_r1 + + + + GSM6928294_r1 + + + + + + SRS16425453 + SAMN32679348 + GSM6928294 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005540 + GSM6928293_r1 + + GSM6928293: R046, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425452 + GSM6928293 + + + + GSM6928293 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425452 + SAMN32679349 + GSM6928293 + + R046, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425452 + SAMN32679349 + GSM6928293 + + + + + + + SRR23052109 + GSM6928293_r1 + + + + GSM6928293_r1 + + + + + + SRS16425452 + SAMN32679349 + GSM6928293 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005539 + GSM6928292_r1 + + GSM6928292: R045, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425451 + GSM6928292 + + + + GSM6928292 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425451 + SAMN32679350 + GSM6928292 + + R045, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425451 + SAMN32679350 + GSM6928292 + + + + + + + SRR23052110 + GSM6928292_r1 + + + + GSM6928292_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425451 + SAMN32679350 + GSM6928292 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052111 + GSM6928292_r2 + + + + GSM6928292_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425451 + SAMN32679350 + GSM6928292 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005538 + GSM6928291_r1 + + GSM6928291: R044, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425450 + GSM6928291 + + + + GSM6928291 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425450 + SAMN32679351 + GSM6928291 + + R044, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425450 + SAMN32679351 + GSM6928291 + + + + + + + SRR23052112 + GSM6928291_r1 + + + + GSM6928291_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425450 + SAMN32679351 + GSM6928291 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052113 + GSM6928291_r2 + + + + GSM6928291_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425450 + SAMN32679351 + GSM6928291 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005537 + GSM6928290_r1 + + GSM6928290: R043, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425448 + GSM6928290 + + + + GSM6928290 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425448 + SAMN32679352 + GSM6928290 + + R043, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425448 + SAMN32679352 + GSM6928290 + + + + + + + SRR23052114 + GSM6928290_r1 + + + + GSM6928290_r1 + + + + + + SRS16425448 + SAMN32679352 + GSM6928290 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005536 + GSM6928289_r1 + + GSM6928289: R042, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425449 + GSM6928289 + + + + GSM6928289 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425449 + SAMN32679353 + GSM6928289 + + R042, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425449 + SAMN32679353 + GSM6928289 + + + + + + + SRR23052115 + GSM6928289_r1 + + + + GSM6928289_r1 + + + + + + SRS16425449 + SAMN32679353 + GSM6928289 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005535 + GSM6928288_r1 + + GSM6928288: R041, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425447 + GSM6928288 + + + + GSM6928288 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425447 + SAMN32679354 + GSM6928288 + + R041, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425447 + SAMN32679354 + GSM6928288 + + + + + + + SRR23052116 + GSM6928288_r1 + + + + GSM6928288_r1 + + + + + + SRS16425447 + SAMN32679354 + GSM6928288 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005534 + GSM6928287_r1 + + GSM6928287: R040, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425446 + GSM6928287 + + + + GSM6928287 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425446 + SAMN32679355 + GSM6928287 + + R040, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425446 + SAMN32679355 + GSM6928287 + + + + + + + SRR23052117 + GSM6928287_r1 + + + + GSM6928287_r1 + + + + + + SRS16425446 + SAMN32679355 + GSM6928287 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005533 + GSM6928286_r1 + + GSM6928286: R039, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425445 + GSM6928286 + + + + GSM6928286 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425445 + SAMN32679356 + GSM6928286 + + R039, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425445 + SAMN32679356 + GSM6928286 + + + + + + + SRR23052118 + GSM6928286_r1 + + + + GSM6928286_r1 + + + + + + SRS16425445 + SAMN32679356 + GSM6928286 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005532 + GSM6928285_r1 + + GSM6928285: R037, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425444 + GSM6928285 + + + + GSM6928285 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425444 + SAMN32679357 + GSM6928285 + + R037, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425444 + SAMN32679357 + GSM6928285 + + + + + + + SRR23052119 + GSM6928285_r1 + + + + GSM6928285_r1 + + + + + + SRS16425444 + SAMN32679357 + GSM6928285 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005531 + GSM6928284_r1 + + GSM6928284: R035, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425443 + GSM6928284 + + + + GSM6928284 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425443 + SAMN32679358 + GSM6928284 + + R035, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425443 + SAMN32679358 + GSM6928284 + + + + + + + SRR23052120 + GSM6928284_r1 + + + + GSM6928284_r1 + + + + + + SRS16425443 + SAMN32679358 + GSM6928284 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005530 + GSM6928283_r1 + + GSM6928283: R033, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425442 + GSM6928283 + + + + GSM6928283 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425442 + SAMN32679359 + GSM6928283 + + R033, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425442 + SAMN32679359 + GSM6928283 + + + + + + + SRR23052121 + GSM6928283_r1 + + + + GSM6928283_r1 + + + + + + SRS16425442 + SAMN32679359 + GSM6928283 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005529 + GSM6928282_r1 + + GSM6928282: R032, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425441 + GSM6928282 + + + + GSM6928282 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425441 + SAMN32679360 + GSM6928282 + + R032, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425441 + SAMN32679360 + GSM6928282 + + + + + + + SRR23052122 + GSM6928282_r1 + + + + GSM6928282_r1 + + + + + + SRS16425441 + SAMN32679360 + GSM6928282 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005528 + GSM6928281_r1 + + GSM6928281: R031, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425440 + GSM6928281 + + + + GSM6928281 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425440 + SAMN32679361 + GSM6928281 + + R031, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425440 + SAMN32679361 + GSM6928281 + + + + + + + SRR23052123 + GSM6928281_r1 + + + + GSM6928281_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425440 + SAMN32679361 + GSM6928281 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052124 + GSM6928281_r2 + + + + GSM6928281_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425440 + SAMN32679361 + GSM6928281 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005527 + GSM6928280_r1 + + GSM6928280: R029, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425439 + GSM6928280 + + + + GSM6928280 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425439 + SAMN32679362 + GSM6928280 + + R029, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425439 + SAMN32679362 + GSM6928280 + + + + + + + SRR23052125 + GSM6928280_r1 + + + + GSM6928280_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425439 + SAMN32679362 + GSM6928280 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052126 + GSM6928280_r2 + + + + GSM6928280_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425439 + SAMN32679362 + GSM6928280 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005526 + GSM6928279_r1 + + GSM6928279: R028, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425438 + GSM6928279 + + + + GSM6928279 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425438 + SAMN32679363 + GSM6928279 + + R028, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425438 + SAMN32679363 + GSM6928279 + + + + + + + SRR23052127 + GSM6928279_r1 + + + + GSM6928279_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425438 + SAMN32679363 + GSM6928279 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052128 + GSM6928279_r2 + + + + GSM6928279_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425438 + SAMN32679363 + GSM6928279 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005525 + GSM6928278_r1 + + GSM6928278: R026, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425436 + GSM6928278 + + + + GSM6928278 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425436 + SAMN32679364 + GSM6928278 + + R026, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425436 + SAMN32679364 + GSM6928278 + + + + + + + SRR23052129 + GSM6928278_r1 + + + + GSM6928278_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425436 + SAMN32679364 + GSM6928278 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005524 + GSM6928277_r1 + + GSM6928277: R025, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425437 + GSM6928277 + + + + GSM6928277 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425437 + SAMN32679365 + GSM6928277 + + R025, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425437 + SAMN32679365 + GSM6928277 + + + + + + + SRR23052130 + GSM6928277_r1 + + + + GSM6928277_r1 + + + + + + SRS16425437 + SAMN32679365 + GSM6928277 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005523 + GSM6928276_r1 + + GSM6928276: R024, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425435 + GSM6928276 + + + + GSM6928276 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425435 + SAMN32679366 + GSM6928276 + + R024, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425435 + SAMN32679366 + GSM6928276 + + + + + + + SRR23052131 + GSM6928276_r1 + + + + GSM6928276_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425435 + SAMN32679366 + GSM6928276 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052132 + GSM6928276_r2 + + + + GSM6928276_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425435 + SAMN32679366 + GSM6928276 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005522 + GSM6928275_r1 + + GSM6928275: R023, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425434 + GSM6928275 + + + + GSM6928275 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425434 + SAMN32679367 + GSM6928275 + + R023, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425434 + SAMN32679367 + GSM6928275 + + + + + + + SRR23052133 + GSM6928275_r1 + + + + GSM6928275_r1 + + + + + + SRS16425434 + SAMN32679367 + GSM6928275 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005521 + GSM6928274_r1 + + GSM6928274: R022, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425433 + GSM6928274 + + + + GSM6928274 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425433 + SAMN32679368 + GSM6928274 + + R022, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425433 + SAMN32679368 + GSM6928274 + + + + + + + SRR23052134 + GSM6928274_r1 + + + + GSM6928274_r1 + + + + + + SRS16425433 + SAMN32679368 + GSM6928274 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005520 + GSM6928273_r1 + + GSM6928273: R020, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425432 + GSM6928273 + + + + GSM6928273 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425432 + SAMN32679369 + GSM6928273 + + R020, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425432 + SAMN32679369 + GSM6928273 + + + + + + + SRR23052135 + GSM6928273_r1 + + + + GSM6928273_r1 + + + + + + SRS16425432 + SAMN32679369 + GSM6928273 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005519 + GSM6928272_r1 + + GSM6928272: R019, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425431 + GSM6928272 + + + + GSM6928272 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425431 + SAMN32679370 + GSM6928272 + + R019, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425431 + SAMN32679370 + GSM6928272 + + + + + + + SRR23052136 + GSM6928272_r1 + + + + GSM6928272_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425431 + SAMN32679370 + GSM6928272 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052137 + GSM6928272_r2 + + + + GSM6928272_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425431 + SAMN32679370 + GSM6928272 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005518 + GSM6928271_r1 + + GSM6928271: R018, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425430 + GSM6928271 + + + + GSM6928271 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425430 + SAMN32679371 + GSM6928271 + + R018, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425430 + SAMN32679371 + GSM6928271 + + + + + + + SRR23052138 + GSM6928271_r1 + + + + GSM6928271_r1 + + + + + + SRS16425430 + SAMN32679371 + GSM6928271 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005517 + GSM6928270_r1 + + GSM6928270: R017, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425429 + GSM6928270 + + + + GSM6928270 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425429 + SAMN32679372 + GSM6928270 + + R017, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425429 + SAMN32679372 + GSM6928270 + + + + + + + SRR23052139 + GSM6928270_r1 + + + + GSM6928270_r1 + + + + + + SRS16425429 + SAMN32679372 + GSM6928270 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005516 + GSM6928269_r1 + + GSM6928269: R016, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425428 + GSM6928269 + + + + GSM6928269 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425428 + SAMN32679373 + GSM6928269 + + R016, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425428 + SAMN32679373 + GSM6928269 + + + + + + + SRR23052140 + GSM6928269_r1 + + + + GSM6928269_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425428 + SAMN32679373 + GSM6928269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052141 + GSM6928269_r2 + + + + GSM6928269_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425428 + SAMN32679373 + GSM6928269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005515 + GSM6928268_r1 + + GSM6928268: R015, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425427 + GSM6928268 + + + + GSM6928268 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425427 + SAMN32679374 + GSM6928268 + + R015, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425427 + SAMN32679374 + GSM6928268 + + + + + + + SRR23052142 + GSM6928268_r1 + + + + GSM6928268_r1 + + + + + + SRS16425427 + SAMN32679374 + GSM6928268 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005514 + GSM6928267_r1 + + GSM6928267: R014, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425426 + GSM6928267 + + + + GSM6928267 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425426 + SAMN32679375 + GSM6928267 + + R014, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425426 + SAMN32679375 + GSM6928267 + + + + + + + SRR23052143 + GSM6928267_r1 + + + + GSM6928267_r1 + + + + + + SRS16425426 + SAMN32679375 + GSM6928267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005513 + GSM6928266_r1 + + GSM6928266: R013, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425425 + GSM6928266 + + + + GSM6928266 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425425 + SAMN32679376 + GSM6928266 + + R013, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425425 + SAMN32679376 + GSM6928266 + + + + + + + SRR23052144 + GSM6928266_r1 + + + + GSM6928266_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425425 + SAMN32679376 + GSM6928266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005512 + GSM6928265_r1 + + GSM6928265: R012, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425424 + GSM6928265 + + + + GSM6928265 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425424 + SAMN32679377 + GSM6928265 + + R012, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425424 + SAMN32679377 + GSM6928265 + + + + + + + SRR23052145 + GSM6928265_r1 + + + + GSM6928265_r1 + + + + + + SRS16425424 + SAMN32679377 + GSM6928265 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005511 + GSM6928264_r1 + + GSM6928264: R009, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425423 + GSM6928264 + + + + GSM6928264 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425423 + SAMN32679378 + GSM6928264 + + R009, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425423 + SAMN32679378 + GSM6928264 + + + + + + + SRR23052146 + GSM6928264_r1 + + + + GSM6928264_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425423 + SAMN32679378 + GSM6928264 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23052147 + GSM6928264_r2 + + + + GSM6928264_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425423 + SAMN32679378 + GSM6928264 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005510 + GSM6928263_r1 + + GSM6928263: R008, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425422 + GSM6928263 + + + + GSM6928263 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425422 + SAMN32679379 + GSM6928263 + + R008, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425422 + SAMN32679379 + GSM6928263 + + + + + + + SRR23052148 + GSM6928263_r1 + + + + GSM6928263_r1 + + + + + + SRS16425422 + SAMN32679379 + GSM6928263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005509 + GSM6928262_r1 + + GSM6928262: R007, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425421 + GSM6928262 + + + + GSM6928262 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425421 + SAMN32679380 + GSM6928262 + + R007, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425421 + SAMN32679380 + GSM6928262 + + + + + + + SRR23052149 + GSM6928262_r1 + + + + GSM6928262_r1 + + + + + + SRS16425421 + SAMN32679380 + GSM6928262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005508 + GSM6928261_r1 + + GSM6928261: R006, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425420 + GSM6928261 + + + + GSM6928261 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425420 + SAMN32679381 + GSM6928261 + + R006, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425420 + SAMN32679381 + GSM6928261 + + + + + + + SRR23052150 + GSM6928261_r1 + + + + GSM6928261_r1 + + + + + + SRS16425420 + SAMN32679381 + GSM6928261 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005507 + GSM6928260_r1 + + GSM6928260: R005, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425419 + GSM6928260 + + + + GSM6928260 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425419 + SAMN32679382 + GSM6928260 + + R005, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425419 + SAMN32679382 + GSM6928260 + + + + + + + SRR23052151 + GSM6928260_r1 + + + + GSM6928260_r1 + + + + + + SRS16425419 + SAMN32679382 + GSM6928260 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005506 + GSM6928259_r1 + + GSM6928259: R004, Control; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425418 + GSM6928259 + + + + GSM6928259 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425418 + SAMN32679383 + GSM6928259 + + R004, Control + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425418 + SAMN32679383 + GSM6928259 + + + + + + + SRR23052152 + GSM6928259_r1 + + + + GSM6928259_r1 + + + + + + SRS16425418 + SAMN32679383 + GSM6928259 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005505 + GSM6928258_r1 + + GSM6928258: R003, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425417 + GSM6928258 + + + + GSM6928258 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425417 + SAMN32679384 + GSM6928258 + + R003, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425417 + SAMN32679384 + GSM6928258 + + + + + + + SRR23052153 + GSM6928258_r1 + + + + GSM6928258_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425417 + SAMN32679384 + GSM6928258 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19005504 + GSM6928257_r1 + + GSM6928257: R001, AMD; Homo sapiens; RNA-Seq + + + SRP417059 + PRJNA922962 + + + + + + + SRS16425415 + GSM6928257 + + + + GSM6928257 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind. We used the Chromium Single Cell 3'v3.1 Reagent Kit according to the manufacturer's protocol. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1573342 + SUB12531165 + + + + Ophthalmology & Visual Sciences, Washington University School of Medicine + +
+ 660 South Euclid Ave, MSC-8096-06-07 + Saint Louis + MO + USA +
+ + Joseph + Lin + + + + + + SRP417059 + PRJNA922962 + GSE222647 + + + scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration + + We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD). Overall design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform. + GSE222647 + + + + + pubmed + 38232696 + + + + + pubmed + 38524380 + + + + + pubmed + 38227383 + + + + + + + SRS16425415 + SAMN32679385 + GSM6928257 + + R001, AMD + + 9606 + Homo sapiens + + + + + bioproject + 922962 + + + + + + + source_name + peripheral blood mononuclear cells + + + tissue + peripheral blood mononuclear cells + + + disease state + AMD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16425415 + SAMN32679385 + GSM6928257 + + + + + + + SRR23052154 + GSM6928257_r1 + + + + GSM6928257_r1 + + + + + loader + fastq-load.py + + + + + + SRS16425415 + SAMN32679385 + GSM6928257 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE226072.xml b/tests/data/GSE226072.xml new file mode 100644 index 0000000..b225ee5 --- /dev/null +++ b/tests/data/GSE226072.xml @@ -0,0 +1,10372 @@ + + + + + + + SRX19498507 + GSM7062651_r1 + + GSM7062651: Male sham sedentary biol rep1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888194 + GSM7062651 + + + + GSM7062651 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888194 + SAMN33438359 + GSM7062651 + + Male sham sedentary biol rep1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888194 + SAMN33438359 + GSM7062651 + + + + + + + SRR23613702 + GSM7062651_r1 + + + + GSM7062651_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888194 + SAMN33438359 + GSM7062651 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498506 + GSM7062650_r1 + + GSM7062650: Female CCI high biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888193 + GSM7062650 + + + + GSM7062650 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888193 + SAMN33438360 + GSM7062650 + + Female CCI high biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888193 + SAMN33438360 + GSM7062650 + + + + + + + SRR23613703 + GSM7062650_r1 + + + + GSM7062650_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888193 + SAMN33438360 + GSM7062650 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498505 + GSM7062649_r1 + + GSM7062649: Female CCI low biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888192 + GSM7062649 + + + + GSM7062649 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888192 + SAMN33438361 + GSM7062649 + + Female CCI low biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888192 + SAMN33438361 + GSM7062649 + + + + + + + SRR23613704 + GSM7062649_r1 + + + + GSM7062649_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888192 + SAMN33438361 + GSM7062649 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498504 + GSM7062648_r1 + + GSM7062648: Female CCI sedentary biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888191 + GSM7062648 + + + + GSM7062648 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888191 + SAMN33438362 + GSM7062648 + + Female CCI sedentary biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888191 + SAMN33438362 + GSM7062648 + + + + + + + SRR23613705 + GSM7062648_r1 + + + + GSM7062648_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888191 + SAMN33438362 + GSM7062648 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498503 + GSM7062647_r1 + + GSM7062647: Female sham sedentary biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888190 + GSM7062647 + + + + GSM7062647 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888190 + SAMN33438363 + GSM7062647 + + Female sham sedentary biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888190 + SAMN33438363 + GSM7062647 + + + + + + + SRR23613706 + GSM7062647_r1 + + + + GSM7062647_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888190 + SAMN33438363 + GSM7062647 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498502 + GSM7062646_r1 + + GSM7062646: Male CCI high biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888189 + GSM7062646 + + + + GSM7062646 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888189 + SAMN33438364 + GSM7062646 + + Male CCI high biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888189 + SAMN33438364 + GSM7062646 + + + + + + + SRR23613707 + GSM7062646_r1 + + + + GSM7062646_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888189 + SAMN33438364 + GSM7062646 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498501 + GSM7062645_r1 + + GSM7062645: Male CCI low biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888188 + GSM7062645 + + + + GSM7062645 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888188 + SAMN33438365 + GSM7062645 + + Male CCI low biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888188 + SAMN33438365 + GSM7062645 + + + + + + + SRR23613708 + GSM7062645_r1 + + + + GSM7062645_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888188 + SAMN33438365 + GSM7062645 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498500 + GSM7062644_r1 + + GSM7062644: Male CCI sedentary biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888187 + GSM7062644 + + + + GSM7062644 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888187 + SAMN33438366 + GSM7062644 + + Male CCI sedentary biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888187 + SAMN33438366 + GSM7062644 + + + + + + + SRR23613709 + GSM7062644_r1 + + + + GSM7062644_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888187 + SAMN33438366 + GSM7062644 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498499 + GSM7062643_r1 + + GSM7062643: Male sham sedentary biol rep 2, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888186 + GSM7062643 + + + + GSM7062643 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888186 + SAMN33438367 + GSM7062643 + + Male sham sedentary biol rep 2, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888186 + SAMN33438367 + GSM7062643 + + + + + + + SRR23613710 + GSM7062643_r1 + + + + GSM7062643_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888186 + SAMN33438367 + GSM7062643 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498498 + GSM7062642_r1 + + GSM7062642: Female CCI high biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888185 + GSM7062642 + + + + GSM7062642 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888185 + SAMN33438368 + GSM7062642 + + Female CCI high biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888185 + SAMN33438368 + GSM7062642 + + + + + + + SRR23613711 + GSM7062642_r1 + + + + GSM7062642_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888185 + SAMN33438368 + GSM7062642 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498497 + GSM7062641_r1 + + GSM7062641: Female CCI low biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888184 + GSM7062641 + + + + GSM7062641 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888184 + SAMN33438369 + GSM7062641 + + Female CCI low biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888184 + SAMN33438369 + GSM7062641 + + + + + + + SRR23613712 + GSM7062641_r1 + + + + GSM7062641_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888184 + SAMN33438369 + GSM7062641 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498496 + GSM7062640_r1 + + GSM7062640: Female CCI sedentary biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888183 + GSM7062640 + + + + GSM7062640 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888183 + SAMN33438370 + GSM7062640 + + Female CCI sedentary biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888183 + SAMN33438370 + GSM7062640 + + + + + + + SRR23613713 + GSM7062640_r1 + + + + GSM7062640_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888183 + SAMN33438370 + GSM7062640 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498495 + GSM7062639_r1 + + GSM7062639: Female sham sedentary biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888182 + GSM7062639 + + + + GSM7062639 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888182 + SAMN33438371 + GSM7062639 + + Female sham sedentary biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888182 + SAMN33438371 + GSM7062639 + + + + + + + SRR23613714 + GSM7062639_r1 + + + + GSM7062639_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888182 + SAMN33438371 + GSM7062639 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498494 + GSM7062638_r1 + + GSM7062638: Male CCI high biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888181 + GSM7062638 + + + + GSM7062638 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888181 + SAMN33438372 + GSM7062638 + + Male CCI high biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888181 + SAMN33438372 + GSM7062638 + + + + + + + SRR23613715 + GSM7062638_r1 + + + + GSM7062638_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888181 + SAMN33438372 + GSM7062638 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498493 + GSM7062637_r1 + + GSM7062637: Male CCI low biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888180 + GSM7062637 + + + + GSM7062637 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888180 + SAMN33438373 + GSM7062637 + + Male CCI low biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888180 + SAMN33438373 + GSM7062637 + + + + + + + SRR23613716 + GSM7062637_r1 + + + + GSM7062637_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888180 + SAMN33438373 + GSM7062637 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498492 + GSM7062636_r1 + + GSM7062636: Male CCI sedentary biol rep 1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888179 + GSM7062636 + + + + GSM7062636 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888179 + SAMN33438374 + GSM7062636 + + Male CCI sedentary biol rep 1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888179 + SAMN33438374 + GSM7062636 + + + + + + + SRR23613717 + GSM7062636_r1 + + + + GSM7062636_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888179 + SAMN33438374 + GSM7062636 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498491 + GSM7062659_r1 + + GSM7062659: Male sham sedentary biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888178 + GSM7062659 + + + + GSM7062659 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888178 + SAMN33438351 + GSM7062659 + + Male sham sedentary biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888178 + SAMN33438351 + GSM7062659 + + + + + + + SRR23613718 + GSM7062659_r1 + + + + GSM7062659_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888178 + SAMN33438351 + GSM7062659 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498490 + GSM7062658_r1 + + GSM7062658: Female CCI high biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888177 + GSM7062658 + + + + GSM7062658 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888177 + SAMN33438352 + GSM7062658 + + Female CCI high biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888177 + SAMN33438352 + GSM7062658 + + + + + + + SRR23613719 + GSM7062658_r1 + + + + GSM7062658_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888177 + SAMN33438352 + GSM7062658 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498489 + GSM7062657_r1 + + GSM7062657: Female CCI low biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888176 + GSM7062657 + + + + GSM7062657 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888176 + SAMN33438353 + GSM7062657 + + Female CCI low biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888176 + SAMN33438353 + GSM7062657 + + + + + + + SRR23613720 + GSM7062657_r1 + + + + GSM7062657_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888176 + SAMN33438353 + GSM7062657 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498488 + GSM7062656_r1 + + GSM7062656: Female CCI sedentary biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888175 + GSM7062656 + + + + GSM7062656 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888175 + SAMN33438354 + GSM7062656 + + Female CCI sedentary biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888175 + SAMN33438354 + GSM7062656 + + + + + + + SRR23613721 + GSM7062656_r1 + + + + GSM7062656_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888175 + SAMN33438354 + GSM7062656 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498487 + GSM7062655_r1 + + GSM7062655: Female sham sedentary biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888174 + GSM7062655 + + + + GSM7062655 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888174 + SAMN33438355 + GSM7062655 + + Female sham sedentary biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888174 + SAMN33438355 + GSM7062655 + + + + + + + SRR23613722 + GSM7062655_r1 + + + + GSM7062655_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888174 + SAMN33438355 + GSM7062655 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498486 + GSM7062654_r1 + + GSM7062654: Male CCI high biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888173 + GSM7062654 + + + + GSM7062654 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888173 + SAMN33438356 + GSM7062654 + + Male CCI high biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888173 + SAMN33438356 + GSM7062654 + + + + + + + SRR23613723 + GSM7062654_r1 + + + + GSM7062654_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888173 + SAMN33438356 + GSM7062654 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498485 + GSM7062653_r1 + + GSM7062653: Male CCI low biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888171 + GSM7062653 + + + + GSM7062653 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888171 + SAMN33438357 + GSM7062653 + + Male CCI low biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888171 + SAMN33438357 + GSM7062653 + + + + + + + SRR23613724 + GSM7062653_r1 + + + + GSM7062653_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888171 + SAMN33438357 + GSM7062653 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498484 + GSM7062652_r1 + + GSM7062652: Male CCI sedentary biol rep 1, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888172 + GSM7062652 + + + + GSM7062652 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888172 + SAMN33438358 + GSM7062652 + + Male CCI sedentary biol rep 1, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888172 + SAMN33438358 + GSM7062652 + + + + + + + SRR23613725 + GSM7062652_r1 + + + + GSM7062652_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888172 + SAMN33438358 + GSM7062652 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498483 + GSM7062627_r1 + + GSM7062627: Male sham sedentary biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888170 + GSM7062627 + + + + GSM7062627 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888170 + SAMN33438383 + GSM7062627 + + Male sham sedentary biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888170 + SAMN33438383 + GSM7062627 + + + + + + + SRR23613726 + GSM7062627_r1 + + + + GSM7062627_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888170 + SAMN33438383 + GSM7062627 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498482 + GSM7062626_r1 + + GSM7062626: Female CCI high biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888169 + GSM7062626 + + + + GSM7062626 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888169 + SAMN33438384 + GSM7062626 + + Female CCI high biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888169 + SAMN33438384 + GSM7062626 + + + + + + + SRR23613727 + GSM7062626_r1 + + + + GSM7062626_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888169 + SAMN33438384 + GSM7062626 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498481 + GSM7062625_r1 + + GSM7062625: Female CCI low biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888168 + GSM7062625 + + + + GSM7062625 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888168 + SAMN33438385 + GSM7062625 + + Female CCI low biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888168 + SAMN33438385 + GSM7062625 + + + + + + + SRR23613728 + GSM7062625_r1 + + + + GSM7062625_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888168 + SAMN33438385 + GSM7062625 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498480 + GSM7062624_r1 + + GSM7062624: Female CCI sedentary biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888167 + GSM7062624 + + + + GSM7062624 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888167 + SAMN33438386 + GSM7062624 + + Female CCI sedentary biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888167 + SAMN33438386 + GSM7062624 + + + + + + + SRR23613729 + GSM7062624_r1 + + + + GSM7062624_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888167 + SAMN33438386 + GSM7062624 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498479 + GSM7062623_r1 + + GSM7062623: Female sham sedentary biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888166 + GSM7062623 + + + + GSM7062623 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888166 + SAMN33438387 + GSM7062623 + + Female sham sedentary biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888166 + SAMN33438387 + GSM7062623 + + + + + + + SRR23613730 + GSM7062623_r1 + + + + GSM7062623_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888166 + SAMN33438387 + GSM7062623 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498478 + GSM7062622_r1 + + GSM7062622: Male CCI high biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888165 + GSM7062622 + + + + GSM7062622 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888165 + SAMN33438388 + GSM7062622 + + Male CCI high biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888165 + SAMN33438388 + GSM7062622 + + + + + + + SRR23613731 + GSM7062622_r1 + + + + GSM7062622_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888165 + SAMN33438388 + GSM7062622 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498477 + GSM7062621_r1 + + GSM7062621: Male CCI low biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888164 + GSM7062621 + + + + GSM7062621 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888164 + SAMN33438389 + GSM7062621 + + Male CCI low biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888164 + SAMN33438389 + GSM7062621 + + + + + + + SRR23613732 + GSM7062621_r1 + + + + GSM7062621_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888164 + SAMN33438389 + GSM7062621 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498476 + GSM7062620_r1 + + GSM7062620: Male CCI sedentary biol rep 1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888163 + GSM7062620 + + + + GSM7062620 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888163 + SAMN33438390 + GSM7062620 + + Male CCI sedentary biol rep 1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888163 + SAMN33438390 + GSM7062620 + + + + + + + SRR23613733 + GSM7062620_r1 + + + + GSM7062620_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888163 + SAMN33438390 + GSM7062620 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498475 + GSM7062666_r1 + + GSM7062666: Female CCI high biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888162 + GSM7062666 + + + + GSM7062666 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888162 + SAMN33438344 + GSM7062666 + + Female CCI high biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888162 + SAMN33438344 + GSM7062666 + + + + + + + SRR23613734 + GSM7062666_r1 + + + + GSM7062666_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888162 + SAMN33438344 + GSM7062666 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498474 + GSM7062665_r1 + + GSM7062665: Female CCI low biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888161 + GSM7062665 + + + + GSM7062665 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888161 + SAMN33438345 + GSM7062665 + + Female CCI low biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888161 + SAMN33438345 + GSM7062665 + + + + + + + SRR23613735 + GSM7062665_r1 + + + + GSM7062665_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888161 + SAMN33438345 + GSM7062665 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498473 + GSM7062664_r1 + + GSM7062664: Female CCI sedentary biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888160 + GSM7062664 + + + + GSM7062664 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888160 + SAMN33438346 + GSM7062664 + + Female CCI sedentary biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888160 + SAMN33438346 + GSM7062664 + + + + + + + SRR23613736 + GSM7062664_r1 + + + + GSM7062664_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888160 + SAMN33438346 + GSM7062664 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498472 + GSM7062663_r1 + + GSM7062663: Female sham sedentary biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888159 + GSM7062663 + + + + GSM7062663 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888159 + SAMN33438347 + GSM7062663 + + Female sham sedentary biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888159 + SAMN33438347 + GSM7062663 + + + + + + + SRR23613737 + GSM7062663_r1 + + + + GSM7062663_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888159 + SAMN33438347 + GSM7062663 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498471 + GSM7062662_r1 + + GSM7062662: Male CCI high biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888158 + GSM7062662 + + + + GSM7062662 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888158 + SAMN33438348 + GSM7062662 + + Male CCI high biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888158 + SAMN33438348 + GSM7062662 + + + + + + + SRR23613738 + GSM7062662_r1 + + + + GSM7062662_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888158 + SAMN33438348 + GSM7062662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498470 + GSM7062661_r1 + + GSM7062661: Male CCI low biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888157 + GSM7062661 + + + + GSM7062661 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888157 + SAMN33438349 + GSM7062661 + + Male CCI low biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888157 + SAMN33438349 + GSM7062661 + + + + + + + SRR23613739 + GSM7062661_r1 + + + + GSM7062661_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888157 + SAMN33438349 + GSM7062661 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498469 + GSM7062660_r1 + + GSM7062660: Male CCI sedentary biol rep 2, Day3; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888156 + GSM7062660 + + + + GSM7062660 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888156 + SAMN33438350 + GSM7062660 + + Male CCI sedentary biol rep 2, Day3 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888156 + SAMN33438350 + GSM7062660 + + + + + + + SRR23613740 + GSM7062660_r1 + + + + GSM7062660_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888156 + SAMN33438350 + GSM7062660 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498468 + GSM7062635_r1 + + GSM7062635: Male sham sedentary biol rep1, Day2; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888155 + GSM7062635 + + + + GSM7062635 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888155 + SAMN33438375 + GSM7062635 + + Male sham sedentary biol rep1, Day2 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888155 + SAMN33438375 + GSM7062635 + + + + + + + SRR23613741 + GSM7062635_r1 + + + + GSM7062635_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888155 + SAMN33438375 + GSM7062635 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498467 + GSM7062634_r1 + + GSM7062634: Female CCI high biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888154 + GSM7062634 + + + + GSM7062634 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888154 + SAMN33438376 + GSM7062634 + + Female CCI high biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888154 + SAMN33438376 + GSM7062634 + + + + + + + SRR23613742 + GSM7062634_r1 + + + + GSM7062634_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888154 + SAMN33438376 + GSM7062634 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498466 + GSM7062633_r1 + + GSM7062633: Female CCI low biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888153 + GSM7062633 + + + + GSM7062633 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888153 + SAMN33438377 + GSM7062633 + + Female CCI low biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888153 + SAMN33438377 + GSM7062633 + + + + + + + SRR23613743 + GSM7062633_r1 + + + + GSM7062633_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888153 + SAMN33438377 + GSM7062633 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498465 + GSM7062632_r1 + + GSM7062632: Female CCI sedentary biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888152 + GSM7062632 + + + + GSM7062632 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888152 + SAMN33438378 + GSM7062632 + + Female CCI sedentary biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888152 + SAMN33438378 + GSM7062632 + + + + + + + SRR23613744 + GSM7062632_r1 + + + + GSM7062632_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888152 + SAMN33438378 + GSM7062632 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498464 + GSM7062631_r1 + + GSM7062631: Female sham sedentary biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888151 + GSM7062631 + + + + GSM7062631 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888151 + SAMN33438379 + GSM7062631 + + Female sham sedentary biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + female + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888151 + SAMN33438379 + GSM7062631 + + + + + + + SRR23613745 + GSM7062631_r1 + + + + GSM7062631_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888151 + SAMN33438379 + GSM7062631 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498463 + GSM7062630_r1 + + GSM7062630: Male CCI high biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888150 + GSM7062630 + + + + GSM7062630 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888150 + SAMN33438380 + GSM7062630 + + Male CCI high biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + high intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888150 + SAMN33438380 + GSM7062630 + + + + + + + SRR23613746 + GSM7062630_r1 + + + + GSM7062630_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888150 + SAMN33438380 + GSM7062630 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498462 + GSM7062629_r1 + + GSM7062629: Male CCI low biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888149 + GSM7062629 + + + + GSM7062629 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888149 + SAMN33438381 + GSM7062629 + + Male CCI low biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + low intensity + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888149 + SAMN33438381 + GSM7062629 + + + + + + + SRR23613747 + GSM7062629_r1 + + + + GSM7062629_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888149 + SAMN33438381 + GSM7062629 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498461 + GSM7062628_r1 + + GSM7062628: Male CCI sedentary biol rep 2, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888148 + GSM7062628 + + + + GSM7062628 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888148 + SAMN33438382 + GSM7062628 + + Male CCI sedentary biol rep 2, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + controlled cortical impact + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888148 + SAMN33438382 + GSM7062628 + + + + + + + SRR23613748 + GSM7062628_r1 + + + + GSM7062628_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888148 + SAMN33438382 + GSM7062628 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19498460 + GSM7062619_r1 + + GSM7062619: Male sham sedentary biol rep1, Day1; Mus musculus; RNA-Seq + + + SRP424473 + PRJNA938467 + + + + + + + SRS16888147 + GSM7062619 + + + + GSM7062619 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm). The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation. Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS. Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3' Kit v3.1 reagents per manufacturer's instructions to generate barcoded single cell RNAseq libraries. Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer. Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell's RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made. The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI's as per manufacturer's directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape. + + + + + NextSeq 2000 + + + + + + SRA1595867 + SUB12915452 + + + + Neuroscience, West Virginia University + +
+ 108 Biomedical Rd BMRC 322 + Morgantown + WV + USA +
+ + Kate + Karelina + + + + + + SRP424473 + PRJNA938467 + GSE226072 + + + Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury. + + In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males. Overall design: A 3mm perilesional coronal brain section was dissected from the ipsilateral hemisphere, and a block containing hippocampal and cortical tissue was then further dissected from that section. Single nuclei RNA sequencing was performed on a NextSeq 2000. + GSE226072 + + + + + pubmed + 37479019 + + + + + + + SRS16888147 + SAMN33438391 + GSM7062619 + + Male sham sedentary biol rep1, Day1 + + 10090 + Mus musculus + + + + + bioproject + 938467 + + + + + + + source_name + brain + + + tissue + brain + + + strain + Swiss Webster + + + age + 4-6 weeks old + + + Sex + male + + + injury + sham + + + exercise + sedentary + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16888147 + SAMN33438391 + GSM7062619 + + + + + + + SRR23613749 + GSM7062619_r1 + + + + GSM7062619_r1 + + + + + loader + fastq-load.py + + + + + + SRS16888147 + SAMN33438391 + GSM7062619 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE226822.xml b/tests/data/GSE226822.xml new file mode 100644 index 0000000..718029d --- /dev/null +++ b/tests/data/GSE226822.xml @@ -0,0 +1,3473 @@ + + + + + + + SRX19582452 + GSM7084230_r1 + + GSM7084230: VC,20Hz,1hr,08; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965335 + GSM7084230 + + + + GSM7084230 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965335 + SAMN33612911 + GSM7084230 + + VC,20Hz,1hr,08 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 20Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965335 + SAMN33612911 + GSM7084230 + + + + + + + SRR23721564 + GSM7084230_r1 + + + + GSM7084230_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965335 + SAMN33612911 + GSM7084230 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721566 + GSM7084230_r2 + + + + GSM7084230_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965335 + SAMN33612911 + GSM7084230 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582451 + GSM7084231_r1 + + GSM7084231: VC,40Hz,1hr,09; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965334 + GSM7084231 + + + + GSM7084231 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965334 + SAMN33612910 + GSM7084231 + + VC,40Hz,1hr,09 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 40Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965334 + SAMN33612910 + GSM7084231 + + + + + + + SRR23721565 + GSM7084231_r1 + + + + GSM7084231_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965334 + SAMN33612910 + GSM7084231 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721568 + GSM7084231_r2 + + + + GSM7084231_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965334 + SAMN33612910 + GSM7084231 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582450 + GSM7084232_r1 + + GSM7084232: VC,40Hz,1hr,10; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965332 + GSM7084232 + + + + GSM7084232 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965332 + SAMN33612909 + GSM7084232 + + VC,40Hz,1hr,10 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 40Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965332 + SAMN33612909 + GSM7084232 + + + + + + + SRR23721567 + GSM7084232_r1 + + + + GSM7084232_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965332 + SAMN33612909 + GSM7084232 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721570 + GSM7084232_r2 + + + + GSM7084232_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965332 + SAMN33612909 + GSM7084232 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582449 + GSM7084233_r1 + + GSM7084233: VC,40Hz,1hr,11; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965333 + GSM7084233 + + + + GSM7084233 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965333 + SAMN33612908 + GSM7084233 + + VC,40Hz,1hr,11 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 40Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965333 + SAMN33612908 + GSM7084233 + + + + + + + SRR23721569 + GSM7084233_r1 + + + + GSM7084233_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965333 + SAMN33612908 + GSM7084233 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721572 + GSM7084233_r2 + + + + GSM7084233_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965333 + SAMN33612908 + GSM7084233 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582448 + GSM7084234_r1 + + GSM7084234: VC,40Hz,1hr,12; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965331 + GSM7084234 + + + + GSM7084234 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965331 + SAMN33612907 + GSM7084234 + + VC,40Hz,1hr,12 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 40Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965331 + SAMN33612907 + GSM7084234 + + + + + + + SRR23721571 + GSM7084234_r1 + + + + GSM7084234_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965331 + SAMN33612907 + GSM7084234 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721575 + GSM7084234_r2 + + + + GSM7084234_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965331 + SAMN33612907 + GSM7084234 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582447 + GSM7084229_r1 + + GSM7084229: VC,20Hz,1hr,07; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965328 + GSM7084229 + + + + GSM7084229 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965328 + SAMN33612912 + GSM7084229 + + VC,20Hz,1hr,07 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 20Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965328 + SAMN33612912 + GSM7084229 + + + + + + + SRR23721573 + GSM7084229_r1 + + + + GSM7084229_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965328 + SAMN33612912 + GSM7084229 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721574 + GSM7084229_r2 + + + + GSM7084229_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965328 + SAMN33612912 + GSM7084229 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582446 + GSM7084228_r1 + + GSM7084228: VC,20Hz,1hr,06; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965329 + GSM7084228 + + + + GSM7084228 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965329 + SAMN33612913 + GSM7084228 + + VC,20Hz,1hr,06 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 20Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965329 + SAMN33612913 + GSM7084228 + + + + + + + SRR23721576 + GSM7084228_r1 + + + + GSM7084228_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965329 + SAMN33612913 + GSM7084228 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721577 + GSM7084228_r2 + + + + GSM7084228_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965329 + SAMN33612913 + GSM7084228 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582445 + GSM7084227_r1 + + GSM7084227: VC,20Hz,1hr,05; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965330 + GSM7084227 + + + + GSM7084227 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965330 + SAMN33612914 + GSM7084227 + + VC,20Hz,1hr,05 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + 20Hz AV flicker + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965330 + SAMN33612914 + GSM7084227 + + + + + + + SRR23721578 + GSM7084227_r1 + + + + GSM7084227_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965330 + SAMN33612914 + GSM7084227 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721579 + GSM7084227_r2 + + + + GSM7084227_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965330 + SAMN33612914 + GSM7084227 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582444 + GSM7084226_r1 + + GSM7084226: VC,Light,1hr,04; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965327 + GSM7084226 + + + + GSM7084226 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965327 + SAMN33612915 + GSM7084226 + + VC,Light,1hr,04 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + ambient light + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965327 + SAMN33612915 + GSM7084226 + + + + + + + SRR23721580 + GSM7084226_r1 + + + + GSM7084226_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965327 + SAMN33612915 + GSM7084226 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721581 + GSM7084226_r2 + + + + GSM7084226_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965327 + SAMN33612915 + GSM7084226 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582443 + GSM7084225_r1 + + GSM7084225: VC,Light,1hr,03; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965324 + GSM7084225 + + + + GSM7084225 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965324 + SAMN33612916 + GSM7084225 + + VC,Light,1hr,03 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + ambient light + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965324 + SAMN33612916 + GSM7084225 + + + + + + + SRR23721582 + GSM7084225_r1 + + + + GSM7084225_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965324 + SAMN33612916 + GSM7084225 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721583 + GSM7084225_r2 + + + + GSM7084225_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965324 + SAMN33612916 + GSM7084225 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582442 + GSM7084224_r1 + + GSM7084224: VC,Light,1hr,02; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965325 + GSM7084224 + + + + GSM7084224 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965325 + SAMN33612917 + GSM7084224 + + VC,Light,1hr,02 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + ambient light + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965325 + SAMN33612917 + GSM7084224 + + + + + + + SRR23721584 + GSM7084224_r1 + + + + GSM7084224_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965325 + SAMN33612917 + GSM7084224 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721585 + GSM7084224_r2 + + + + GSM7084224_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965325 + SAMN33612917 + GSM7084224 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19582441 + GSM7084223_r1 + + GSM7084223: VC,Light,1hr,01; Mus musculus; RNA-Seq + + + SRP426001 + PRJNA941839 + + + + + + + SRS16965326 + GSM7084223 + + + + GSM7084223 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction 10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells + + + + + Illumina NovaSeq 6000 + + + + + + SRA1601712 + SUB12939830 + + + + Georgia Institute of Technology + +
+ 315 Ferst Dr NW Rm 3303 + Atlanta + GA + USA +
+ + Levi + Wood + + + + + + SRP426001 + PRJNA941839 + GSE226822 + + + Brain rhythms control microglial response and cytokine expression via NFkB signaling + + Microglia, the brain's primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes. Overall design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4) + GSE226822 + + + + + pubmed + 37556553 + + + + + + + SRS16965326 + SAMN33612918 + GSM7084223 + + VC,Light,1hr,01 + + 10090 + Mus musculus + + + + + bioproject + 941839 + + + + + + + source_name + Visual Cortex, Right Hemisphere + + + tissue + Visual Cortex, Right Hemisphere + + + age + 2mo + + + Sex + male + + + genotype + WT + + + treatment + ambient light + + + duration + 1hr + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS16965326 + SAMN33612918 + GSM7084223 + + + + + + + SRR23721586 + GSM7084223_r1 + + + + GSM7084223_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965326 + SAMN33612918 + GSM7084223 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23721587 + GSM7084223_r2 + + + + GSM7084223_r1 + + + + + loader + fastq-load.py + + + + + + SRS16965326 + SAMN33612918 + GSM7084223 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE227515.xml b/tests/data/GSE227515.xml new file mode 100644 index 0000000..a24d1ef --- /dev/null +++ b/tests/data/GSE227515.xml @@ -0,0 +1,3743 @@ + + + + + + + SRX19693498 + GSM7102033_r1 + + GSM7102033: Long-term DR; Hippocampus Sample 3 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062438 + GSM7102033 + + + + GSM7102033 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062438 + SAMN33786670 + GSM7102033 + + Long-term DR; Hippocampus Sample 3 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Long-term dietary restriction + + + age + 24 months + + + + + + + SRS17062438 + SAMN33786670 + GSM7102033 + + + + + + + SRR23881481 + GSM7102033_r1 + + + + GSM7102033_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062438 + SAMN33786670 + GSM7102033 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881486 + GSM7102033_r2 + + + + GSM7102033_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062438 + SAMN33786670 + GSM7102033 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693497 + GSM7102034_r1 + + GSM7102034: Long-term DR; Hippocampus Sample 4 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062437 + GSM7102034 + + + + GSM7102034 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062437 + SAMN33786669 + GSM7102034 + + Long-term DR; Hippocampus Sample 4 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Long-term dietary restriction + + + age + 24 months + + + + + + + SRS17062437 + SAMN33786669 + GSM7102034 + + + + + + + SRR23881482 + GSM7102034_r1 + + + + GSM7102034_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062437 + SAMN33786669 + GSM7102034 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881485 + GSM7102034_r2 + + + + GSM7102034_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062437 + SAMN33786669 + GSM7102034 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693493 + GSM7102031_r1 + + GSM7102031: Long-term DR; Hippocampus Sample 1 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062433 + GSM7102031 + + + + GSM7102031 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062433 + SAMN33786672 + GSM7102031 + + Long-term DR; Hippocampus Sample 1 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Long-term dietary restriction + + + age + 24 months + + + + + + + SRS17062433 + SAMN33786672 + GSM7102031 + + + + + + + SRR23881488 + GSM7102031_r2 + + + + GSM7102031_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062433 + SAMN33786672 + GSM7102031 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881491 + GSM7102031_r1 + + + + GSM7102031_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062433 + SAMN33786672 + GSM7102031 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693492 + GSM7102027_r1 + + GSM7102027: AL; Hippocampus Sample 4 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062432 + GSM7102027 + + + + GSM7102027 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062432 + SAMN33786676 + GSM7102027 + + AL; Hippocampus Sample 4 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 24 months + + + + + + + SRS17062432 + SAMN33786676 + GSM7102027 + + + + + + + SRR23881492 + GSM7102027_r1 + + + + GSM7102027_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062432 + SAMN33786676 + GSM7102027 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881500 + GSM7102027_r2 + + + + GSM7102027_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062432 + SAMN33786676 + GSM7102027 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693491 + GSM7102032_r1 + + GSM7102032: Long-term DR; Hippocampus Sample 2 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062431 + GSM7102032 + + + + GSM7102032 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062431 + SAMN33786671 + GSM7102032 + + Long-term DR; Hippocampus Sample 2 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Long-term dietary restriction + + + age + 24 months + + + + + + + SRS17062431 + SAMN33786671 + GSM7102032 + + + + + + + SRR23881487 + GSM7102032_r2 + + + + GSM7102032_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062431 + SAMN33786671 + GSM7102032 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881493 + GSM7102032_r1 + + + + GSM7102032_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062431 + SAMN33786671 + GSM7102032 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693490 + GSM7102025_r1 + + GSM7102025: AL; Hippocampus Sample 2 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062430 + GSM7102025 + + + + GSM7102025 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062430 + SAMN33786678 + GSM7102025 + + AL; Hippocampus Sample 2 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 24 months + + + + + + + SRS17062430 + SAMN33786678 + GSM7102025 + + + + + + + SRR23881494 + GSM7102025_r1 + + + + GSM7102025_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062430 + SAMN33786678 + GSM7102025 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881511 + GSM7102025_r2 + + + + GSM7102025_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062430 + SAMN33786678 + GSM7102025 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693489 + GSM7102024_r1 + + GSM7102024: AL; Hippocampus Sample 1 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062429 + GSM7102024 + + + + GSM7102024 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062429 + SAMN33786679 + GSM7102024 + + AL; Hippocampus Sample 1 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 24 months + + + + + + + SRS17062429 + SAMN33786679 + GSM7102024 + + + + + + + SRR23881495 + GSM7102024_r1 + + + + GSM7102024_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062429 + SAMN33786679 + GSM7102024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881510 + GSM7102024_r2 + + + + GSM7102024_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062429 + SAMN33786679 + GSM7102024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693487 + GSM7102023_r1 + + GSM7102023: Acute DR; Hippocampus Sample 3 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062427 + GSM7102023 + + + + GSM7102023 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062427 + SAMN33786680 + GSM7102023 + + Acute DR; Hippocampus Sample 3 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Acute dietary restriction + + + age + 24 months + + + + + + + SRS17062427 + SAMN33786680 + GSM7102023 + + + + + + + SRR23881503 + GSM7102023_r1 + + + + GSM7102023_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062427 + SAMN33786680 + GSM7102023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881508 + GSM7102023_r2 + + + + GSM7102023_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062427 + SAMN33786680 + GSM7102023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881509 + GSM7102023_r3 + + + + GSM7102023_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062427 + SAMN33786680 + GSM7102023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693486 + GSM7102021_r1 + + GSM7102021: Acute DR; Hippocampus Sample 1 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062426 + GSM7102021 + + + + GSM7102021 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062426 + SAMN33786682 + GSM7102021 + + Acute DR; Hippocampus Sample 1 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Acute dietary restriction + + + age + 24 months + + + + + + + SRS17062426 + SAMN33786682 + GSM7102021 + + + + + + + SRR23881504 + GSM7102021_r1 + + + + GSM7102021_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062426 + SAMN33786682 + GSM7102021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881505 + GSM7102021_r2 + + + + GSM7102021_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062426 + SAMN33786682 + GSM7102021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693485 + GSM7102022_r1 + + GSM7102022: Acute DR; Hippocampus Sample 2 24 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062425 + GSM7102022 + + + + GSM7102022 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1617752 + SUB13054797 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062425 + SAMN33786681 + GSM7102022 + + Acute DR; Hippocampus Sample 2 24 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Acute dietary restriction + + + age + 24 months + + + + + + + SRS17062425 + SAMN33786681 + GSM7102022 + + + + + + + SRR23881506 + GSM7102022_r1 + + + + GSM7102022_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062425 + SAMN33786681 + GSM7102022 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881507 + GSM7102022_r2 + + + + GSM7102022_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062425 + SAMN33786681 + GSM7102022 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693496 + GSM7102029_r1 + + GSM7102029: AL; Hippocampus Sample 2 5 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062436 + GSM7102029 + + + + GSM7102029 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1606519 + SUB12960574 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062436 + SAMN33786674 + GSM7102029 + + AL; Hippocampus Sample 2 5 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 5 months + + + + + + + SRS17062436 + SAMN33786674 + GSM7102029 + + + + + + + SRR23881483 + GSM7102029_r1 + + + + GSM7102029_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062436 + SAMN33786674 + GSM7102029 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881490 + GSM7102029_r2 + + + + GSM7102029_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062436 + SAMN33786674 + GSM7102029 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881502 + GSM7102029_r3 + + + + GSM7102029_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062436 + SAMN33786674 + GSM7102029 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693495 + GSM7102028_r1 + + GSM7102028: AL; Hippocampus Sample 1 5 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062435 + GSM7102028 + + + + GSM7102028 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1606519 + SUB12960574 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062435 + SAMN33786675 + GSM7102028 + + AL; Hippocampus Sample 1 5 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 5 months + + + + + + + SRS17062435 + SAMN33786675 + GSM7102028 + + + + + + + SRR23881484 + GSM7102028_r1 + + + + GSM7102028_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062435 + SAMN33786675 + GSM7102028 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881499 + GSM7102028_r2 + + + + GSM7102028_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062435 + SAMN33786675 + GSM7102028 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX19693494 + GSM7102030_r1 + + GSM7102030: AL; Hippocampus Sample 3 5 mo; Mus musculus; RNA-Seq + + + SRP427690 + PRJNA945433 + + + + + + + SRS17062434 + GSM7102030 + + + + GSM7102030 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality. Reagents of the Chromium Single Cell 3' GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer's protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3' Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer's protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. 10X Nuc-seq, v3.0 chemistry + + + + + Illumina NovaSeq 6000 + + + + + + SRA1606519 + SUB12960574 + + + + Tony Wyss-Coray, Neurology & Neurological Sciences, Stanford Medicine + +
+ 290 Jane Stanford Way Lab 3E + Stanford + CA + USA +
+ + Oliver + Hahn + + + + + + SRP427690 + PRJNA945433 + GSE227515 + + + Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice + + Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long) and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice. Overall design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain. + GSE227515 + + + + + pubmed + 37591239 + + + + + + + SRS17062434 + SAMN33786673 + GSM7102030 + + AL; Hippocampus Sample 3 5 mo + + 10090 + Mus musculus + + + + + bioproject + 945433 + + + + + + + source_name + Hippocampus + + + Sex + female + + + tissue + Hippocampus + + + strain + C3HB6F1 + + + diet + Ad libitum + + + age + 5 months + + + + + + + SRS17062434 + SAMN33786673 + GSM7102030 + + + + + + + SRR23881489 + GSM7102030_r1 + + + + GSM7102030_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062434 + SAMN33786673 + GSM7102030 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR23881501 + GSM7102030_r2 + + + + GSM7102030_r1 + + + + + loader + fastq-load.py + + + + + + SRS17062434 + SAMN33786673 + GSM7102030 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE230451.xml b/tests/data/GSE230451.xml new file mode 100644 index 0000000..225ffab --- /dev/null +++ b/tests/data/GSE230451.xml @@ -0,0 +1,1572 @@ + + + + + + + SRX20090554 + GSM7224038_r1 + + GSM7224038: U4; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422250 + GSM7224038 + + + + GSM7224038 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422250 + SAMN34357548 + GSM7224038 + + U4 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + USCs treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422250 + SAMN34357548 + GSM7224038 + + + + + + + SRR24295158 + GSM7224038_r1 + + + + GSM7224038_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422250 + SAMN34357548 + GSM7224038 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090553 + GSM7224037_r1 + + GSM7224037: U3; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422249 + GSM7224037 + + + + GSM7224037 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422249 + SAMN34357549 + GSM7224037 + + U3 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + USCs treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422249 + SAMN34357549 + GSM7224037 + + + + + + + SRR24295159 + GSM7224037_r1 + + + + GSM7224037_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422249 + SAMN34357549 + GSM7224037 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090552 + GSM7224036_r1 + + GSM7224036: U2; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422248 + GSM7224036 + + + + GSM7224036 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422248 + SAMN34357550 + GSM7224036 + + U2 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + USCs treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422248 + SAMN34357550 + GSM7224036 + + + + + + + SRR24295160 + GSM7224036_r1 + + + + GSM7224036_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422248 + SAMN34357550 + GSM7224036 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090551 + GSM7224035_r1 + + GSM7224035: U1; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422247 + GSM7224035 + + + + GSM7224035 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422247 + SAMN34357551 + GSM7224035 + + U1 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + USCs treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422247 + SAMN34357551 + GSM7224035 + + + + + + + SRR24295161 + GSM7224035_r1 + + + + GSM7224035_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422247 + SAMN34357551 + GSM7224035 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090550 + GSM7224034_r1 + + GSM7224034: P4; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422245 + GSM7224034 + + + + GSM7224034 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422245 + SAMN34357552 + GSM7224034 + + P4 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + PBS treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422245 + SAMN34357552 + GSM7224034 + + + + + + + SRR24295162 + GSM7224034_r1 + + + + GSM7224034_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422245 + SAMN34357552 + GSM7224034 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090549 + GSM7224033_r1 + + GSM7224033: P3; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422244 + GSM7224033 + + + + GSM7224033 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422244 + SAMN34357553 + GSM7224033 + + P3 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + PBS treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422244 + SAMN34357553 + GSM7224033 + + + + + + + SRR24295163 + GSM7224033_r1 + + + + GSM7224033_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422244 + SAMN34357553 + GSM7224033 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090548 + GSM7224032_r1 + + GSM7224032: P2; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422246 + GSM7224032 + + + + GSM7224032 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422246 + SAMN34357554 + GSM7224032 + + P2 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + PBS treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422246 + SAMN34357554 + GSM7224032 + + + + + + + SRR24295164 + GSM7224032_r1 + + + + GSM7224032_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422246 + SAMN34357554 + GSM7224032 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20090547 + GSM7224031_r1 + + GSM7224031: P1; Mus musculus; RNA-Seq + + + SRP434287 + PRJNA961151 + + + + + + + SRS17422243 + GSM7224031 + + + + GSM7224031 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The hippocampus was carefully dissected out from mice with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1627213 + SUB13173859 + + + + Kunming Medical University + +
+ GuiZhou + KUNMING City + Yunnan + China +
+ + Weixing + Zeng + + + + + + SRP434287 + PRJNA961151 + GSE230451 + + + Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging + + Brain aging is a major risk factor for many brain diseases, which seriously affects the quality of life and even life span, and poses an increasingly serious threat to human health. Research shows that anti-aging and an extra year of life expectancy could bring $38 trillion in economic gains. Therefore, it is urgent to study the mechanism of brain aging, find effective ways to improve aging and improve the quality of life of the aging population. In the early stage, we established the culture system of activated urine stem cells (aUSCs), which can significantly improve the nerve cell senescence in vitro and brain aging of natural aging mice and macaques, suggesting that aUSCs have strong anti-brain aging ability; The results of single-nucleus sequencing of mouse hippocampus suggested that anti-aging was achieved by changing the glial cell subset to constitutively inhibit inflammatory signaling to reduce inflammatory response. Based on this, this topic continues to conduct aUSCs intervention on naturally aging rhesus monkeys to study the anti-brain aging effect and potential mechanism of aUSCs in non-human primates; Meanwhile, the human cerebral organoid model was applied to further study the anti-brain aging effect and potential mechanism of aUSCs in the human brain. Therefore, this topic not only screens seed cells for state-supported stem cell transformation applications, but also provides solutions for the problems caused by world aging, which has great scientific significance and economic value. In order to explore the mechanism of aUSCs anti-brain aging, we used single-cell sequencing to analyze the effect of aUSCs on the hippocampus of aging mice. Overall design: Single-nucleus RNA-sequencing of hippocampus from mouse. + GSE230451 + + + + + SRS17422243 + SAMN34357555 + GSM7224031 + + P1 + + 10090 + Mus musculus + + + + + bioproject + 961151 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + treatment + PBS treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17422243 + SAMN34357555 + GSM7224031 + + + + + + + SRR24295165 + GSM7224031_r1 + + + + GSM7224031_r1 + + + + + loader + fastq-load.py + + + + + + SRS17422243 + SAMN34357555 + GSM7224031 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE232309.xml b/tests/data/GSE232309.xml new file mode 100644 index 0000000..127dd39 --- /dev/null +++ b/tests/data/GSE232309.xml @@ -0,0 +1,1764 @@ + + + + + + + SRX20300906 + GSM7325163_r1 + + GSM7325163: Ovary, 9 months, 8; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626774 + GSM7325163 + + + + GSM7325163 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626774 + SAMN35051602 + GSM7325163 + + Ovary, 9 months, 8 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 9 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626774 + SAMN35051602 + GSM7325163 + + + + + + + SRR24516559 + GSM7325163_r1 + + + + GSM7325163_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626774 + SAMN35051602 + GSM7325163 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300905 + GSM7325162_r1 + + GSM7325162: Ovary, 9 months, 7; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626773 + GSM7325162 + + + + GSM7325162 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626773 + SAMN35051603 + GSM7325162 + + Ovary, 9 months, 7 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 9 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626773 + SAMN35051603 + GSM7325162 + + + + + + + SRR24516560 + GSM7325162_r1 + + + + GSM7325162_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626773 + SAMN35051603 + GSM7325162 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300904 + GSM7325161_r1 + + GSM7325161: Ovary, 9 months, 6; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626772 + GSM7325161 + + + + GSM7325161 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626772 + SAMN35051604 + GSM7325161 + + Ovary, 9 months, 6 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 9 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626772 + SAMN35051604 + GSM7325161 + + + + + + + SRR24516561 + GSM7325161_r1 + + + + GSM7325161_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626772 + SAMN35051604 + GSM7325161 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300903 + GSM7325160_r1 + + GSM7325160: Ovary, 9 months, 5; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626771 + GSM7325160 + + + + GSM7325160 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626771 + SAMN35051605 + GSM7325160 + + Ovary, 9 months, 5 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 9 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626771 + SAMN35051605 + GSM7325160 + + + + + + + SRR24516562 + GSM7325160_r1 + + + + GSM7325160_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626771 + SAMN35051605 + GSM7325160 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300902 + GSM7325159_r1 + + GSM7325159: Ovary, 3 months, 4; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626770 + GSM7325159 + + + + GSM7325159 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626770 + SAMN35051606 + GSM7325159 + + Ovary, 3 months, 4 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 3 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626770 + SAMN35051606 + GSM7325159 + + + + + + + SRR24516563 + GSM7325159_r1 + + + + GSM7325159_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626770 + SAMN35051606 + GSM7325159 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300901 + GSM7325158_r1 + + GSM7325158: Ovary, 3 months, 3; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626769 + GSM7325158 + + + + GSM7325158 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626769 + SAMN35051607 + GSM7325158 + + Ovary, 3 months, 3 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 3 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626769 + SAMN35051607 + GSM7325158 + + + + + + + SRR24516564 + GSM7325158_r1 + + + + GSM7325158_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626769 + SAMN35051607 + GSM7325158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300900 + GSM7325157_r1 + + GSM7325157: Ovary, 3 months, 2; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626767 + GSM7325157 + + + + GSM7325157 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626767 + SAMN35051608 + GSM7325157 + + Ovary, 3 months, 2 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 3 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626767 + SAMN35051608 + GSM7325157 + + + + + + + SRR24516565 + GSM7325157_r1 + + + + GSM7325157_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626767 + SAMN35051608 + GSM7325157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20300899 + GSM7325156_r1 + + GSM7325156: Ovary, 3 months, 1; Mus musculus; RNA-Seq + + + SRP437267 + PRJNA971592 + + + + + + + SRS17626768 + GSM7325156 + + + + GSM7325156 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi) scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1636969 + SUB13323229 + + + + Aging and Metabolism, Oklahoma Medical Research Foundation + +
+ 825 N.E. 13th Street + Oklahoma City + OK + USA +
+ + Michael + Stout + + + + + + SRP437267 + PRJNA971592 + GSE232309 + + + A single-cell atlas of the aging murine ovary + + Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes. Overall design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice + GSE232309 + + + + + pubmed + 38200272 + + + + + + + SRS17626768 + SAMN35051609 + GSM7325156 + + Ovary, 3 months, 1 + + 10090 + Mus musculus + + + + + bioproject + 971592 + + + + + + + source_name + ovary + + + tissue + ovary + + + age + 3 months old + + + Sex + female + + + genotype + C57BL6/J + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17626768 + SAMN35051609 + GSM7325156 + + + + + + + SRR24516566 + GSM7325156_r1 + + + + GSM7325156_r1 + + + + + loader + fastq-load.py + + + + + + SRS17626768 + SAMN35051609 + GSM7325156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE233276.xml b/tests/data/GSE233276.xml new file mode 100644 index 0000000..fc3924d --- /dev/null +++ b/tests/data/GSE233276.xml @@ -0,0 +1,2236 @@ + + + + + + + SRX20494962 + GSM7421519_r1 + + GSM7421519: Post-RTX remission, donor 4, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804698 + GSM7421519 + + + + GSM7421519 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804698 + SAMN35342310 + GSM7421519 + + Post-RTX remission, donor 4, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Remission + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804698 + SAMN35342310 + GSM7421519 + + + + + + + SRR24716302 + GSM7421519_r1 + + + + GSM7421519_r1 + + + + + + SRS17804698 + SAMN35342310 + GSM7421519 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716303 + GSM7421519_r2 + + + + GSM7421519_r1 + + + + + + SRS17804698 + SAMN35342310 + GSM7421519 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494961 + GSM7421518_r1 + + GSM7421518: Post-RTX relapse, donor 4, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804697 + GSM7421518 + + + + GSM7421518 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804697 + SAMN35342311 + GSM7421518 + + Post-RTX relapse, donor 4, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Relapse + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804697 + SAMN35342311 + GSM7421518 + + + + + + + SRR24716304 + GSM7421518_r1 + + + + GSM7421518_r1 + + + + + + SRS17804697 + SAMN35342311 + GSM7421518 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716305 + GSM7421518_r2 + + + + GSM7421518_r1 + + + + + + SRS17804697 + SAMN35342311 + GSM7421518 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494960 + GSM7421517_r1 + + GSM7421517: Post-RTX remission, donor 3, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804696 + GSM7421517 + + + + GSM7421517 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804696 + SAMN35342312 + GSM7421517 + + Post-RTX remission, donor 3, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Remission + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804696 + SAMN35342312 + GSM7421517 + + + + + + + SRR24716306 + GSM7421517_r1 + + + + GSM7421517_r1 + + + + + + SRS17804696 + SAMN35342312 + GSM7421517 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716307 + GSM7421517_r2 + + + + GSM7421517_r1 + + + + + + SRS17804696 + SAMN35342312 + GSM7421517 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494959 + GSM7421516_r1 + + GSM7421516: Post-RTX relapse, donor 3, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804694 + GSM7421516 + + + + GSM7421516 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804694 + SAMN35342313 + GSM7421516 + + Post-RTX relapse, donor 3, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Relapse + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804694 + SAMN35342313 + GSM7421516 + + + + + + + SRR24716308 + GSM7421516_r1 + + + + GSM7421516_r1 + + + + + + SRS17804694 + SAMN35342313 + GSM7421516 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716309 + GSM7421516_r2 + + + + GSM7421516_r1 + + + + + + SRS17804694 + SAMN35342313 + GSM7421516 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494958 + GSM7421515_r1 + + GSM7421515: Post-RTX remission, donor 2, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804695 + GSM7421515 + + + + GSM7421515 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804695 + SAMN35342314 + GSM7421515 + + Post-RTX remission, donor 2, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Remission + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804695 + SAMN35342314 + GSM7421515 + + + + + + + SRR24716310 + GSM7421515_r1 + + + + GSM7421515_r1 + + + + + + SRS17804695 + SAMN35342314 + GSM7421515 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716311 + GSM7421515_r2 + + + + GSM7421515_r1 + + + + + + SRS17804695 + SAMN35342314 + GSM7421515 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494957 + GSM7421514_r1 + + GSM7421514: Post-RTX relapse, donor 2, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804693 + GSM7421514 + + + + GSM7421514 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804693 + SAMN35342315 + GSM7421514 + + Post-RTX relapse, donor 2, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + male + + + disease state + Relapse + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804693 + SAMN35342315 + GSM7421514 + + + + + + + SRR24716312 + GSM7421514_r1 + + + + GSM7421514_r1 + + + + + + SRS17804693 + SAMN35342315 + GSM7421514 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716313 + GSM7421514_r2 + + + + GSM7421514_r1 + + + + + + SRS17804693 + SAMN35342315 + GSM7421514 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494956 + GSM7421513_r1 + + GSM7421513: Post-RTX remission, donor 1, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804692 + GSM7421513 + + + + GSM7421513 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804692 + SAMN35342316 + GSM7421513 + + Post-RTX remission, donor 1, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + female + + + disease state + Remission + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804692 + SAMN35342316 + GSM7421513 + + + + + + + SRR24716314 + GSM7421513_r1 + + + + GSM7421513_r1 + + + + + + SRS17804692 + SAMN35342316 + GSM7421513 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716315 + GSM7421513_r2 + + + + GSM7421513_r1 + + + + + + SRS17804692 + SAMN35342316 + GSM7421513 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20494955 + GSM7421512_r1 + + GSM7421512: Post-RTX relapse, donor 1, scRNAseq; Homo sapiens; RNA-Seq + + + SRP439226 + PRJNA975613 + + + + + + + SRS17804691 + GSM7421512 + + + + GSM7421512 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5' v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5' V1.1 reagents. Complementary DNA (cDNA) and 5' gene expression libraries were generated using the standard 10x Genomics protocol. 5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1643504 + SUB13455054 + + + + McGill University + +
+ 1001 boulevard Decarie + Montreal + Quebec + Canada +
+ + Tho-Alfakar + Al-Aubodah + + + + + + SRP439226 + PRJNA975613 + GSE233276 + + + Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem] + + An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS. Overall design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq). + GSE233276 + + + + + pubmed + 37996443 + + + + + + parent_bioproject + PRJNA975612 + + + + + + SRS17804691 + SAMN35342317 + GSM7421512 + + Post-RTX relapse, donor 1, scRNAseq + + 9606 + Homo sapiens + + + + + bioproject + 975613 + + + + + + + source_name + Blood + + + tissue + Blood + + + cell type + B cells + + + age + Pediatric + + + Sex + female + + + disease state + Relapse + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17804691 + SAMN35342317 + GSM7421512 + + + + + + + SRR24716316 + GSM7421512_r1 + + + + GSM7421512_r1 + + + + + + SRS17804691 + SAMN35342317 + GSM7421512 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24716317 + GSM7421512_r2 + + + + GSM7421512_r1 + + + + + + SRS17804691 + SAMN35342317 + GSM7421512 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE234278.xml b/tests/data/GSE234278.xml new file mode 100644 index 0000000..ee5fa38 --- /dev/null +++ b/tests/data/GSE234278.xml @@ -0,0 +1,3452 @@ + + + + + + + SRX20608101 + GSM7461487_r1 + + GSM7461487: control4weeks_A_4; Mus musculus; RNA-Seq + + + SRP441402 + PRJNA980678 + + + + + + + SRS17908025 + GSM7461487 + + + + GSM7461487 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from frozen mouse brain tissues were isolated according to the previously published protocol with certain modifications (Sakib et al., 2021 [PMID: 33554149]). Briefly, frozen tissues were Dounce homogenized in 500 µl EZ prep lysis buffer (Sigma NUC101) supplemented with 1:200 RNAse inhibitor (Promega, N2615) for 45 times in a 1.5 mL Eppendorf tube using micro pestles. The volume was increased with lysis buffer up to 2000 µl and incubated on ice for 5 min. Lysates were centrifuged for 5 min at 500 × g at 4 °C and supernatants were discarded. The pellet was resuspended into 2000 µl lysis buffer and incubated for 5 min on ice. After 5 min of centrifugation (500 × g at 4 °C), the resulting pellet was resuspended into 1500 µl nuclei suspension buffer (NSB, 0.5 % BSA, 1:100 Roche protease inhibitor, 1:200 RNAse inhibitor in 1×PBS) and centrifuged again for 5 min (500 × g at 4 °C). The pellet was finally resuspended into 500 µl NSB and stained with 7AAD (Invitrogen, Cat: 00-6993-50). Single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter. Approximately 4000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3ʹ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei. 10X genomics snRNA-seq + + + + + NextSeq 550 + + + + + + SRA1650341 + SUB13503739 + + + + Epigenetics and Systems Medicine in Neurodegenerative Diseases, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) + +
+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908025 + SAMN35652844 + GSM7461487 + + control4weeks_A_4 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908025 + SAMN35652844 + GSM7461487 + + + + + + + SRR24843880 + GSM7461487_r1 + + + + GSM7461487_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908025 + SAMN35652844 + GSM7461487 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24843891 + GSM7461487_r4 + + + + GSM7461487_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908025 + SAMN35652844 + GSM7461487 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24843892 + GSM7461487_r3 + + + + GSM7461487_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908025 + SAMN35652844 + GSM7461487 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908029 + SAMN35652841 + GSM7461490 + + exercise4weeks_B_3 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + exercise + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908029 + SAMN35652841 + GSM7461490 + + + + + + + SRR24843882 + GSM7461490_r1 + + + + GSM7461490_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908029 + SAMN35652841 + GSM7461490 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908027 + SAMN35652840 + GSM7461491 + + exercise4weeks_B_4 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + exercise + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908027 + SAMN35652840 + GSM7461491 + + + + + + + SRR24843886 + GSM7461491_r1 + + + + GSM7461491_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908027 + SAMN35652840 + GSM7461491 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908028 + SAMN35652843 + GSM7461488 + + exercise4weeks_B_1 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + exercise + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908028 + SAMN35652843 + GSM7461488 + + + + + + + SRR24843890 + GSM7461488_r1 + + + + GSM7461488_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908028 + SAMN35652843 + GSM7461488 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908018 + SAMN35652842 + GSM7461489 + + exercise4weeks_B_2 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + exercise + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908018 + SAMN35652842 + GSM7461489 + + + + + + + SRR24843883 + GSM7461489_r4 + + + + GSM7461489_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908018 + SAMN35652842 + GSM7461489 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX20608096 + GSM7461486_r1 + + GSM7461486: control4weeks_A_3; Mus musculus; RNA-Seq + + + SRP441402 + PRJNA980678 + + + + + + + SRS17908021 + GSM7461486 + + + + GSM7461486 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from frozen mouse brain tissues were isolated according to the previously published protocol with certain modifications (Sakib et al., 2021 [PMID: 33554149]). Briefly, frozen tissues were Dounce homogenized in 500 µl EZ prep lysis buffer (Sigma NUC101) supplemented with 1:200 RNAse inhibitor (Promega, N2615) for 45 times in a 1.5 mL Eppendorf tube using micro pestles. The volume was increased with lysis buffer up to 2000 µl and incubated on ice for 5 min. Lysates were centrifuged for 5 min at 500 × g at 4 °C and supernatants were discarded. The pellet was resuspended into 2000 µl lysis buffer and incubated for 5 min on ice. After 5 min of centrifugation (500 × g at 4 °C), the resulting pellet was resuspended into 1500 µl nuclei suspension buffer (NSB, 0.5 % BSA, 1:100 Roche protease inhibitor, 1:200 RNAse inhibitor in 1×PBS) and centrifuged again for 5 min (500 × g at 4 °C). The pellet was finally resuspended into 500 µl NSB and stained with 7AAD (Invitrogen, Cat: 00-6993-50). Single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter. Approximately 4000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3ʹ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei. 10X genomics snRNA-seq + + + + + NextSeq 550 + + + + + + SRA1650341 + SUB13503739 + + + + Epigenetics and Systems Medicine in Neurodegenerative Diseases, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) + +
+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908021 + SAMN35652845 + GSM7461486 + + control4weeks_A_3 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908021 + SAMN35652845 + GSM7461486 + + + + + + + SRR24843881 + GSM7461486_r4 + + + + GSM7461486_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908021 + SAMN35652845 + GSM7461486 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR24843899 + GSM7461486_r3 + + + + GSM7461486_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908021 + SAMN35652845 + GSM7461486 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20608095 + GSM7461485_r1 + + GSM7461485: control4weeks_A_2; Mus musculus; RNA-Seq + + + SRP441402 + PRJNA980678 + + + + + + + SRS17908026 + GSM7461485 + + + + GSM7461485 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from frozen mouse brain tissues were isolated according to the previously published protocol with certain modifications (Sakib et al., 2021 [PMID: 33554149]). Briefly, frozen tissues were Dounce homogenized in 500 µl EZ prep lysis buffer (Sigma NUC101) supplemented with 1:200 RNAse inhibitor (Promega, N2615) for 45 times in a 1.5 mL Eppendorf tube using micro pestles. The volume was increased with lysis buffer up to 2000 µl and incubated on ice for 5 min. Lysates were centrifuged for 5 min at 500 × g at 4 °C and supernatants were discarded. The pellet was resuspended into 2000 µl lysis buffer and incubated for 5 min on ice. After 5 min of centrifugation (500 × g at 4 °C), the resulting pellet was resuspended into 1500 µl nuclei suspension buffer (NSB, 0.5 % BSA, 1:100 Roche protease inhibitor, 1:200 RNAse inhibitor in 1×PBS) and centrifuged again for 5 min (500 × g at 4 °C). The pellet was finally resuspended into 500 µl NSB and stained with 7AAD (Invitrogen, Cat: 00-6993-50). Single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter. Approximately 4000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3ʹ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei. 10X genomics snRNA-seq + + + + + NextSeq 550 + + + + + + SRA1650341 + SUB13503739 + + + + Epigenetics and Systems Medicine in Neurodegenerative Diseases, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) + +
+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908026 + SAMN35652846 + GSM7461485 + + control4weeks_A_2 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908026 + SAMN35652846 + GSM7461485 + + + + + + + SRR24843904 + GSM7461485_r1 + + + + GSM7461485_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908026 + SAMN35652846 + GSM7461485 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR24843906 + GSM7461485_r3 + + + + GSM7461485_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908026 + SAMN35652846 + GSM7461485 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR24843907 + GSM7461485_r4 + + + + GSM7461485_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908026 + SAMN35652846 + GSM7461485 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20608094 + GSM7461484_r1 + + GSM7461484: control4weeks_A_1; Mus musculus; RNA-Seq + + + SRP441402 + PRJNA980678 + + + + + + + SRS17908020 + GSM7461484 + + + + GSM7461484 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from frozen mouse brain tissues were isolated according to the previously published protocol with certain modifications (Sakib et al., 2021 [PMID: 33554149]). Briefly, frozen tissues were Dounce homogenized in 500 µl EZ prep lysis buffer (Sigma NUC101) supplemented with 1:200 RNAse inhibitor (Promega, N2615) for 45 times in a 1.5 mL Eppendorf tube using micro pestles. The volume was increased with lysis buffer up to 2000 µl and incubated on ice for 5 min. Lysates were centrifuged for 5 min at 500 × g at 4 °C and supernatants were discarded. The pellet was resuspended into 2000 µl lysis buffer and incubated for 5 min on ice. After 5 min of centrifugation (500 × g at 4 °C), the resulting pellet was resuspended into 1500 µl nuclei suspension buffer (NSB, 0.5 % BSA, 1:100 Roche protease inhibitor, 1:200 RNAse inhibitor in 1×PBS) and centrifuged again for 5 min (500 × g at 4 °C). The pellet was finally resuspended into 500 µl NSB and stained with 7AAD (Invitrogen, Cat: 00-6993-50). Single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter. Approximately 4000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3ʹ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei. 10X genomics snRNA-seq + + + + + NextSeq 550 + + + + + + SRA1650341 + SUB13503739 + + + + Epigenetics and Systems Medicine in Neurodegenerative Diseases, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) + +
+ Von-Siebold-Str. 3a + Göttingen + Niedersachsen + Germany +
+ + André + Fischer + + + + + + SRP441402 + PRJNA980678 + GSE234278 + + + A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise + + Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-?B, Wnt/ß-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline. Overall design: 8 WT adult mice were divided into 2 equally sized groups - runners that had free and voluntary access to running wheels in their cages (the 'exercise' group), and sedentary mice that had similar wheels in their cages that were however blocked (the 'control' group). This voluntary exercise paradigm lasted 4 weeks, after which whole hippocampal nuclei were isolated from all mice for snRNA-seq analysis. + GSE234278 + + + + + pubmed + 38217668 + + + + + + + SRS17908020 + SAMN35652847 + GSM7461484 + + control4weeks_A_1 + + 10090 + Mus musculus + + + + + bioproject + 980678 + + + + + + + source_name + whole hippocampus, tissue from adult mice brain + + + tissue + whole hippocampus, tissue from adult mice brain + + + strain + C57BL/6J , WT + + + treatment + control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17908020 + SAMN35652847 + GSM7461484 + + + + + + + SRR24843908 + GSM7461484_r1 + + + + GSM7461484_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908020 + SAMN35652847 + GSM7461484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR24843911 + GSM7461484_r4 + + + + GSM7461484_r1 + + + + + loader + fastq-load.py + + + + + + SRS17908020 + SAMN35652847 + GSM7461484 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE234419.xml b/tests/data/GSE234419.xml new file mode 100644 index 0000000..8869241 --- /dev/null +++ b/tests/data/GSE234419.xml @@ -0,0 +1,1069 @@ + + + + + + + SRX20631942 + GSM7467236_r1 + + GSM7467236: Tmem119-creERT2-cGaswt/wt microglia mouse 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP441695 + PRJNA981208 + + + + + + + SRS17930970 + GSM7467236 + + + + GSM7467236 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651019 + SUB13507739 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441695 + PRJNA981208 + GSE234419 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration II + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. + GSE234419 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17930970 + SAMN35667939 + GSM7467236 + + Tmem119-creERT2-cGaswt/wt microglia mouse 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981208 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17930970 + SAMN35667939 + GSM7467236 + + + + + + + SRR24867996 + GSM7467236_r1 + + + + GSM7467236_r1 + + + + + loader + fastq-load.py + + + + + + SRS17930970 + SAMN35667939 + GSM7467236 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631941 + GSM7467235_r1 + + GSM7467235: Tmem119-creERT2-cGaswt/wt microglia mouse 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP441695 + PRJNA981208 + + + + + + + SRS17930969 + GSM7467235 + + + + GSM7467235 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651019 + SUB13507739 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441695 + PRJNA981208 + GSE234419 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration II + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. + GSE234419 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17930969 + SAMN35667940 + GSM7467235 + + Tmem119-creERT2-cGaswt/wt microglia mouse 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981208 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17930969 + SAMN35667940 + GSM7467235 + + + + + + + SRR24867997 + GSM7467235_r1 + + + + GSM7467235_r1 + + + + + loader + fastq-load.py + + + + + + SRS17930969 + SAMN35667940 + GSM7467235 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631940 + GSM7467234_r1 + + GSM7467234: Tmem119-creERT2-cGaswt/wt microglia mouse 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP441695 + PRJNA981208 + + + + + + + SRS17930971 + GSM7467234 + + + + GSM7467234 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651019 + SUB13507739 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441695 + PRJNA981208 + GSE234419 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration II + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. + GSE234419 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17930971 + SAMN35667941 + GSM7467234 + + Tmem119-creERT2-cGaswt/wt microglia mouse 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981208 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17930971 + SAMN35667941 + GSM7467234 + + + + + + + SRR24867998 + GSM7467234_r1 + + + + GSM7467234_r1 + + + + + loader + fastq-load.py + + + + + + SRS17930971 + SAMN35667941 + GSM7467234 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631939 + GSM7467233_r1 + + GSM7467233: Tmem119-creERT2-cGaswt/R241E microglia mouse 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP441695 + PRJNA981208 + + + + + + + SRS17930968 + GSM7467233 + + + + GSM7467233 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651019 + SUB13507739 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441695 + PRJNA981208 + GSE234419 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration II + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. + GSE234419 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17930968 + SAMN35667942 + GSM7467233 + + Tmem119-creERT2-cGaswt/R241E microglia mouse 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981208 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17930968 + SAMN35667942 + GSM7467233 + + + + + + + SRR24867999 + GSM7467233_r1 + + + + GSM7467233_r1 + + + + + loader + fastq-load.py + + + + + + SRS17930968 + SAMN35667942 + GSM7467233 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631938 + GSM7467232_r1 + + GSM7467232: Tmem119-creERT2-cGaswt/R241E microglia mouse 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP441695 + PRJNA981208 + + + + + + + SRS17930967 + GSM7467232 + + + + GSM7467232 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. Sorted nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651019 + SUB13507739 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441695 + PRJNA981208 + GSE234419 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration II + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647. + GSE234419 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17930967 + SAMN35667943 + GSM7467232 + + Tmem119-creERT2-cGaswt/R241E microglia mouse 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981208 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17930967 + SAMN35667943 + GSM7467232 + + + + + + + SRR24868000 + GSM7467232_r1 + + + + GSM7467232_r1 + + + + + loader + fastq-load.py + + + + + + SRS17930967 + SAMN35667943 + GSM7467232 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE234421.xml b/tests/data/GSE234421.xml new file mode 100644 index 0000000..36efce2 --- /dev/null +++ b/tests/data/GSE234421.xml @@ -0,0 +1,1708 @@ + + + + + + + SRX20631983 + GSM7467275_r1 + + GSM7467275: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931011 + GSM7467275 + + + + GSM7467275 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931011 + SAMN35668012 + GSM7467275 + + Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931011 + SAMN35668012 + GSM7467275 + + + + + + + SRR24868034 + GSM7467275_r1 + + + + GSM7467275_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931011 + SAMN35668012 + GSM7467275 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631982 + GSM7467274_r1 + + GSM7467274: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931008 + GSM7467274 + + + + GSM7467274 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931008 + SAMN35668013 + GSM7467274 + + Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931008 + SAMN35668013 + GSM7467274 + + + + + + + SRR24868035 + GSM7467274_r1 + + + + GSM7467274_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931008 + SAMN35668013 + GSM7467274 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631981 + GSM7467273_r1 + + GSM7467273: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931007 + GSM7467273 + + + + GSM7467273 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931007 + SAMN35668014 + GSM7467273 + + Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931007 + SAMN35668014 + GSM7467273 + + + + + + + SRR24868036 + GSM7467273_r1 + + + + GSM7467273_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931007 + SAMN35668014 + GSM7467273 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631980 + GSM7467272_r1 + + GSM7467272: Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931009 + GSM7467272 + + + + GSM7467272 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931009 + SAMN35668015 + GSM7467272 + + Tmem119-creERT2-cGaswt/wt microglia whole brain mouse 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931009 + SAMN35668015 + GSM7467272 + + + + + + + SRR24868037 + GSM7467272_r1 + + + + GSM7467272_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931009 + SAMN35668015 + GSM7467272 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631979 + GSM7467271_r1 + + GSM7467271: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931010 + GSM7467271 + + + + GSM7467271 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931010 + SAMN35668016 + GSM7467271 + + Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931010 + SAMN35668016 + GSM7467271 + + + + + + + SRR24868038 + GSM7467271_r1 + + + + GSM7467271_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931010 + SAMN35668016 + GSM7467271 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631978 + GSM7467270_r1 + + GSM7467270: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931006 + GSM7467270 + + + + GSM7467270 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931006 + SAMN35668017 + GSM7467270 + + Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931006 + SAMN35668017 + GSM7467270 + + + + + + + SRR24868039 + GSM7467270_r1 + + + + GSM7467270_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931006 + SAMN35668017 + GSM7467270 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631977 + GSM7467269_r1 + + GSM7467269: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931004 + GSM7467269 + + + + GSM7467269 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931004 + SAMN35668018 + GSM7467269 + + Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931004 + SAMN35668018 + GSM7467269 + + + + + + + SRR24868040 + GSM7467269_r1 + + + + GSM7467269_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931004 + SAMN35668018 + GSM7467269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20631976 + GSM7467268_r1 + + GSM7467268: Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP441697 + PRJNA981209 + + + + + + + SRS17931005 + GSM7467268 + + + + GSM7467268 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were then loaded into a Chromium Single Cell Controller. ChromiumSingle Cell 3' Library & Gel Bead Kit v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1651011 + SUB13507728 + + + + Ablasser, EPFL + +
+ route Cantonale + Lausanne + Switzerland +
+ + Andrea + Ablasser + + + + + + SRP441697 + PRJNA981209 + GSE234421 + + + cGAS/STING drives ageing-related inflammation and neurodegeneration IV + + Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age. Overall design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. + GSE234421 + + + + + pubmed + 37532932 + + + + + + parent_bioproject + PRJNA981203 + + + + + + SRS17931005 + SAMN35668019 + GSM7467268 + + Tmem119-creERT2-cGaswt/R241E microglia whole brain mouse 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 981209 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + cell type + microglia + + + genotype + cGasR241E + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS17931005 + SAMN35668019 + GSM7467268 + + + + + + + SRR24868041 + GSM7467268_r1 + + + + GSM7467268_r1 + + + + + loader + fastq-load.py + + + + + + SRS17931005 + SAMN35668019 + GSM7467268 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE235193.xml b/tests/data/GSE235193.xml new file mode 100644 index 0000000..03e6cdf --- /dev/null +++ b/tests/data/GSE235193.xml @@ -0,0 +1,1276 @@ + + + + + + + SRX20710819 + GSM7496626_r1 + + GSM7496626: Hippocampus, pre-onset 3, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003555 + GSM7496626 + + + + GSM7496626 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003555 + SAMN35778241 + GSM7496626 + + Hippocampus, pre-onset 3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8aN1768D/+ + + + strain + C57BL/6J + + + batch + 2 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003555 + SAMN35778241 + GSM7496626 + + + + + + + SRR24952767 + GSM7496626_r1 + + + + GSM7496626_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003555 + SAMN35778241 + GSM7496626 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20710818 + GSM7496625_r1 + + GSM7496625: Hippocampus, pre-onset 2, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003556 + GSM7496625 + + + + GSM7496625 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003556 + SAMN35778242 + GSM7496625 + + Hippocampus, pre-onset 2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8aN1768D/+ + + + strain + C57BL/6J + + + batch + 2 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003556 + SAMN35778242 + GSM7496625 + + + + + + + SRR24952768 + GSM7496625_r1 + + + + GSM7496625_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003556 + SAMN35778242 + GSM7496625 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20710817 + GSM7496624_r1 + + GSM7496624: Hippocampus, pre-onset 1, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003554 + GSM7496624 + + + + GSM7496624 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003554 + SAMN35778243 + GSM7496624 + + Hippocampus, pre-onset 1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8aN1768D/+ + + + strain + C57BL/6J + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003554 + SAMN35778243 + GSM7496624 + + + + + + + SRR24952769 + GSM7496624_r1 + + + + GSM7496624_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003554 + SAMN35778243 + GSM7496624 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20710816 + GSM7496623_r1 + + GSM7496623: Hippocampus, control 3, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003552 + GSM7496623 + + + + GSM7496623 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003552 + SAMN35778244 + GSM7496623 + + Hippocampus, control 3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8a+/+ + + + strain + C57BL/6J + + + batch + 2 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003552 + SAMN35778244 + GSM7496623 + + + + + + + SRR24952770 + GSM7496623_r1 + + + + GSM7496623_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003552 + SAMN35778244 + GSM7496623 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20710815 + GSM7496622_r1 + + GSM7496622: Hippocampus, control 2, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003553 + GSM7496622 + + + + GSM7496622 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003553 + SAMN35778245 + GSM7496622 + + Hippocampus, control 2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8a+/+ + + + strain + C57BL/6J + + + batch + 2 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003553 + SAMN35778245 + GSM7496622 + + + + + + + SRR24952771 + GSM7496622_r1 + + + + GSM7496622_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003553 + SAMN35778245 + GSM7496622 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20710814 + GSM7496621_r1 + + GSM7496621: Hippocampus, control 1, snRNAseq; Mus musculus; RNA-Seq + + + SRP444479 + PRJNA984742 + + + + + + + SRS18003551 + GSM7496621 + + + + GSM7496621 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl­2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer. Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3' gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1657699 + SUB13551322 + + + + Meisler Lab, Human Genetics, University of Michigan + +
+ 1241 E. Catherine St + Ann Arbor + MI + USA +
+ + Sophie + Hill + + + + + + SRP444479 + PRJNA984742 + GSE235193 + + + Long-term downregulation of SCN8A in mouse models of developmental and epileptic encephalopathy + + De novo mutations of the voltage-gated sodium channel SCN8A cause severe developmental and epileptic encephalopathy (DEE). Since pathogenic variants have gain-of-function effects on SCN8A activity, reduction of SCN8A expression is an effective therapeutic strategy. We previously described an antisense oligonucleotide (ASO) that delays seizure onset in a mouse model of SCN8A-DEE when administered at postnatal day 2. To investigate the potential effectiveness of post-onset ASO treatment, we first examined the extent of differential gene expression in hippocampus during the pre-onset period. Hippocampal single-nucleus RNA-sequencing detected only minor expression changes after the two month pre-seizure period. ASO treatments that were initiated after seizure onset were protective in the Scn8a mutant mice during the 12 month observation period. As an alternative treatment for down-regulation of Scn8a, we administered a single dose of an AAV10 virus expressing Scn8a shRNA. The viral shRNA was protective against seizures and lethality during the 12 month observation period. These data indicate that reduction of SCN8A expression, either by repeated administration of ASO or a single dose of shRNA virus, may be effective for longterm control of SCN8A-DEE. Overall design: Nuclei from adult mouse hippocampus were isolated, purified with FACS sorting, and analyzed with single-nucleus RNA-sequencing (10X Genomics 3' gene expression). + GSE235193 + + + + + SRS18003551 + SAMN35778246 + GSM7496621 + + Hippocampus, control 1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 984742 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + age + P50 + + + Sex + female + + + genotype + Scn8a+/+ + + + strain + C57BL/6J + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18003551 + SAMN35778246 + GSM7496621 + + + + + + + SRR24952772 + GSM7496621_r1 + + + + GSM7496621_r1 + + + + + loader + fastq-load.py + + + + + + SRS18003551 + SAMN35778246 + GSM7496621 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE235490.xml b/tests/data/GSE235490.xml new file mode 100644 index 0000000..f22c038 --- /dev/null +++ b/tests/data/GSE235490.xml @@ -0,0 +1,1700 @@ + + + + + + + SRX20741024 + GSM7503689_r1 + + GSM7503689: WT2, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030943 + GSM7503689 + + + + GSM7503689 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030943 + SAMN35820796 + GSM7503689 + + WT2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030943 + SAMN35820796 + GSM7503689 + + + + + + + SRR24984345 + GSM7503689_r1 + + + + GSM7503689_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030943 + SAMN35820796 + GSM7503689 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741023 + GSM7503690_r1 + + GSM7503690: WT3, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030942 + GSM7503690 + + + + GSM7503690 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030942 + SAMN35820795 + GSM7503690 + + WT3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030942 + SAMN35820795 + GSM7503690 + + + + + + + SRR24984346 + GSM7503690_r1 + + + + GSM7503690_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030942 + SAMN35820795 + GSM7503690 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741022 + GSM7503691_r1 + + GSM7503691: WT4, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030941 + GSM7503691 + + + + GSM7503691 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030941 + SAMN35820794 + GSM7503691 + + WT4, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030941 + SAMN35820794 + GSM7503691 + + + + + + + SRR24984347 + GSM7503691_r1 + + + + GSM7503691_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030941 + SAMN35820794 + GSM7503691 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741021 + GSM7503686_r1 + + GSM7503686: KO3, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030940 + GSM7503686 + + + + GSM7503686 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030940 + SAMN35820799 + GSM7503686 + + KO3, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Kdm5a-/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030940 + SAMN35820799 + GSM7503686 + + + + + + + SRR24984348 + GSM7503686_r1 + + + + GSM7503686_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030940 + SAMN35820799 + GSM7503686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741020 + GSM7503687_r1 + + GSM7503687: KO4, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030939 + GSM7503687 + + + + GSM7503687 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030939 + SAMN35820798 + GSM7503687 + + KO4, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Kdm5a-/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030939 + SAMN35820798 + GSM7503687 + + + + + + + SRR24984349 + GSM7503687_r1 + + + + GSM7503687_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030939 + SAMN35820798 + GSM7503687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741019 + GSM7503688_r1 + + GSM7503688: WT1, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030938 + GSM7503688 + + + + GSM7503688 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030938 + SAMN35820797 + GSM7503688 + + WT1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030938 + SAMN35820797 + GSM7503688 + + + + + + + SRR24984350 + GSM7503688_r1 + + + + GSM7503688_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030938 + SAMN35820797 + GSM7503688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741018 + GSM7503685_r1 + + GSM7503685: KO2, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030937 + GSM7503685 + + + + GSM7503685 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030937 + SAMN35820800 + GSM7503685 + + KO2, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Kdm5a-/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030937 + SAMN35820800 + GSM7503685 + + + + + + + SRR24984351 + GSM7503685_r1 + + + + GSM7503685_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030937 + SAMN35820800 + GSM7503685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX20741017 + GSM7503684_r1 + + GSM7503684: KO1, snRNAseq; Mus musculus; RNA-Seq + + + SRP445217 + PRJNA986143 + + + + + + + SRS18030936 + GSM7503684 + + + + GSM7503684 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampi were isolated and, for each animal, a punch was collected from the middle of the hippocampus using a 1 mm diameter tissue punch. The punches were immediately stored at -80oC. For each animal, tissue punches from the right and left hippocampi were combined and homogenized using a glass Dounce homogenizer in 500 ml ice-cold Nuclei EZ lysis buffer (NLB) (NUC-101, Sigma) 25 times with pestle A and then 25 times with pestle B. The mixture was transferred to a pre-chilled Eppendorf tube and 1000 ml of NLB was added to the tube and incubated on ice for 5 minutes (min). The tubes were centrifuged at 800 x g for 5 min at 4o C. The nuclei were resuspended in 75 ml of nuclei suspension buffer (consisting of 1X PBS, 1% BSA (AM2618, Thermo Fisher Scientific), and 0.2 U/ml (1%) Rnase inhibitor (AM2694, Thermo Fisher Scientific)). The nuclei were then filtered through a 40 mm Flowmi Cell Strainer (H13680-0040, Bel-Art) to remove cellular debris. Concentration of nuclei for each sample was calculated using Trypan Blue (T8154, Sigma) on a hemocytometer, aiming for a final concentration of ~1000-2000 nuclei/ml. Single nuclei were processed using the 10X Genomics Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's user guide. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer 2100 (Agilent). The libraries were constructed following TruSeq Stranded mRNA Sample preparation guide (Illumina) and paired end sequencing was performed on the Illumina NovaSeq 6000 platform at the McDermott Center Next Generation Sequencing Core at UTSW. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1659989 + SUB13566503 + + + + Chahrour lab, UT Southwestern Medical Center + +
+ 6000 Harry Hines Boulevard, NB10.104 + Dallas + Texas + USA +
+ + Maria + Chahrour + + + + + + SRP445217 + PRJNA986143 + GSE235490 + + + Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity + + KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity. Overall design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000. + GSE235490 + + + + + pubmed + 37992166 + + + + + + + SRS18030936 + SAMN35820801 + GSM7503684 + + KO1, snRNAseq + + 10090 + Mus musculus + + + + + bioproject + 986143 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + genotype + Kdm5a-/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18030936 + SAMN35820801 + GSM7503684 + + + + + + + SRR24984352 + GSM7503684_r1 + + + + GSM7503684_r1 + + + + + loader + fastq-load.py + + + + + + SRS18030936 + SAMN35820801 + GSM7503684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE237816.xml b/tests/data/GSE237816.xml new file mode 100644 index 0000000..7759ee1 --- /dev/null +++ b/tests/data/GSE237816.xml @@ -0,0 +1,5032 @@ + + + + + + + SRX21100473 + GSM7653945_r1 + + GSM7653945: S858R Kidney 6 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369681 + GSM7653945 + + + + GSM7653945 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + S858R Kidney 6 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + + + + + + SRR25361084 + GSM7653945_r1 + + + + GSM7653945_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361085 + GSM7653945_r2 + + + + GSM7653945_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361086 + GSM7653945_r3 + + + + GSM7653945_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361087 + GSM7653945_r4 + + + + GSM7653945_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369681 + SAMN36637412 + GSM7653945 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100472 + GSM7653944_r1 + + GSM7653944: WT Kidney 5 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369680 + GSM7653944 + + + + GSM7653944 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + WT Kidney 5 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + + + + + + SRR25361088 + GSM7653944_r1 + + + + GSM7653944_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361089 + GSM7653944_r2 + + + + GSM7653944_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361090 + GSM7653944_r3 + + + + GSM7653944_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361091 + GSM7653944_r4 + + + + GSM7653944_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369680 + SAMN36637413 + GSM7653944 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100471 + GSM7653943_r1 + + GSM7653943: S858R Kidney 4 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369679 + GSM7653943 + + + + GSM7653943 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + S858R Kidney 4 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + + + + + + SRR25361092 + GSM7653943_r1 + + + + GSM7653943_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361093 + GSM7653943_r2 + + + + GSM7653943_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361094 + GSM7653943_r3 + + + + GSM7653943_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361095 + GSM7653943_r4 + + + + GSM7653943_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369679 + SAMN36637414 + GSM7653943 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100470 + GSM7653942_r1 + + GSM7653942: WT Kidney 3 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369678 + GSM7653942 + + + + GSM7653942 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + WT Kidney 3 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + + + + + + SRR25361096 + GSM7653942_r1 + + + + GSM7653942_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361097 + GSM7653942_r2 + + + + GSM7653942_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361098 + GSM7653942_r3 + + + + GSM7653942_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361099 + GSM7653942_r4 + + + + GSM7653942_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369678 + SAMN36637415 + GSM7653942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100469 + GSM7653941_r1 + + GSM7653941: S858R Kidney 2 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369677 + GSM7653941 + + + + GSM7653941 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + S858R Kidney 2 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + + + + + + SRR25361100 + GSM7653941_r1 + + + + GSM7653941_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361101 + GSM7653941_r2 + + + + GSM7653941_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361102 + GSM7653941_r3 + + + + GSM7653941_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361123 + GSM7653941_r4 + + + + GSM7653941_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369677 + SAMN36637416 + GSM7653941 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100468 + GSM7653940_r1 + + GSM7653940: WT Kidney 1 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369676 + GSM7653940 + + + + GSM7653940 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + WT Kidney 1 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right kidney + + + tissue + right kidney + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + + + + + + SRR25361103 + GSM7653940_r1 + + + + GSM7653940_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361104 + GSM7653940_r2 + + + + GSM7653940_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361105 + GSM7653940_r3 + + + + GSM7653940_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361122 + GSM7653940_r4 + + + + GSM7653940_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369676 + SAMN36637417 + GSM7653940 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100467 + GSM7653939_r1 + + GSM7653939: S858R Cortex 15 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369675 + GSM7653939 + + + + GSM7653939 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + S858R Cortex 15 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + + + + + + SRR25361106 + GSM7653939_r1 + + + + GSM7653939_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361107 + GSM7653939_r2 + + + + GSM7653939_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361108 + GSM7653939_r3 + + + + GSM7653939_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361121 + GSM7653939_r4 + + + + GSM7653939_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369675 + SAMN36637418 + GSM7653939 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100466 + GSM7653938_r1 + + GSM7653938: S858R Cortex 13 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369674 + GSM7653938 + + + + GSM7653938 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + S858R Cortex 13 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + + + + + + SRR25361109 + GSM7653938_r1 + + + + GSM7653938_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361110 + GSM7653938_r2 + + + + GSM7653938_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361111 + GSM7653938_r3 + + + + GSM7653938_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361120 + GSM7653938_r4 + + + + GSM7653938_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369674 + SAMN36637419 + GSM7653938 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100465 + GSM7653936_r1 + + GSM7653936: WT Cortex 3 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369673 + GSM7653936 + + + + GSM7653936 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + WT Cortex 3 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + + + + + + SRR25361112 + GSM7653936_r1 + + + + GSM7653936_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361113 + GSM7653936_r2 + + + + GSM7653936_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361114 + GSM7653936_r3 + + + + GSM7653936_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361115 + GSM7653936_r4 + + + + GSM7653936_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369673 + SAMN36637421 + GSM7653936 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100464 + GSM7653937_r1 + + GSM7653937: WT Cortex 4 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369672 + GSM7653937 + + + + GSM7653937 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + WT Cortex 4 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + + + + + + SRR25361116 + GSM7653937_r1 + + + + GSM7653937_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361117 + GSM7653937_r2 + + + + GSM7653937_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361118 + GSM7653937_r3 + + + + GSM7653937_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361119 + GSM7653937_r4 + + + + GSM7653937_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369672 + SAMN36637420 + GSM7653937 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100463 + GSM7653935_r1 + + GSM7653935: WT Cortex 2 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369671 + GSM7653935 + + + + GSM7653935 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + WT Cortex 2 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + C57BL6/J control + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + + + + + + SRR25361124 + GSM7653935_r1 + + + + GSM7653935_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361125 + GSM7653935_r2 + + + + GSM7653935_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361126 + GSM7653935_r3 + + + + GSM7653935_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361127 + GSM7653935_r4 + + + + GSM7653935_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369671 + SAMN36637422 + GSM7653935 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21100462 + GSM7653934_r1 + + GSM7653934: S858R Cortex 1 snRNA-seq; Mus musculus; RNA-Seq + + + SRP450505 + PRJNA996862 + + + + + + + SRS18369670 + GSM7653934 + + + + GSM7653934 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020. We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1676694 + SUB13697964 + + + + Lasseigne Lab, Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham + +
+ 1900 University Boulevard + Birmingham + AL + USA +
+ + Jordan + Whitlock + + + + + + SRP450505 + PRJNA996862 + GSE237816 + + + Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice + + Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS. Grant Number: 1U54oD030167 UAB Pilot Center for Precision Animal Modeling (C-PAM) Grantee: Brittany Lasseigne Grant Number: 5T32GM008111-35 UAB CMDB T32 Grantee: Jordan Whitlock Overall design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664) + GSE237816 + + + + + pubmed + 37872881 + + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + S858R Cortex 1 snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 996862 + + + + + + + source_name + right cerebral cortex + + + tissue + right cerebral cortex + + + genotype + S858R + + + age + 6 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + + + + + + SRR25361128 + GSM7653934_r1 + + + + GSM7653934_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361129 + GSM7653934_r2 + + + + GSM7653934_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361130 + GSM7653934_r3 + + + + GSM7653934_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25361131 + GSM7653934_r4 + + + + GSM7653934_r1 + + + + + loader + fastq-load.py + + + + + + SRS18369670 + SAMN36637423 + GSM7653934 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE240687.xml b/tests/data/GSE240687.xml new file mode 100644 index 0000000..b739c88 --- /dev/null +++ b/tests/data/GSE240687.xml @@ -0,0 +1,1620 @@ + + + + + + + SRX21346828 + GSM7707563_r1 + + GSM7707563: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 4, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591887 + GSM7707563 + + + + GSM7707563 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591887 + SAMN36953933 + GSM7707563 + + 5XFAD.Cpa3Cre/+ (MC KO), bio rep 4, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3Cre/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591887 + SAMN36953933 + GSM7707563 + + + + + + + SRR25619896 + GSM7707563_r1 + + + + GSM7707563_r1 + + + + + + SRS18591887 + SAMN36953933 + GSM7707563 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346827 + GSM7707562_r1 + + GSM7707562: 5XFAD.Cpa3+/+ (MC WT), bio rep 4, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591888 + GSM7707562 + + + + GSM7707562 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591888 + SAMN36953934 + GSM7707562 + + 5XFAD.Cpa3+/+ (MC WT), bio rep 4, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3+/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591888 + SAMN36953934 + GSM7707562 + + + + + + + SRR25619897 + GSM7707562_r1 + + + + GSM7707562_r1 + + + + + + SRS18591888 + SAMN36953934 + GSM7707562 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346826 + GSM7707561_r1 + + GSM7707561: 5XFAD.Cpa3+/+ (MC WT), bio rep 3, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591886 + GSM7707561 + + + + GSM7707561 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591886 + SAMN36953935 + GSM7707561 + + 5XFAD.Cpa3+/+ (MC WT), bio rep 3, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3+/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591886 + SAMN36953935 + GSM7707561 + + + + + + + SRR25619898 + GSM7707561_r1 + + + + GSM7707561_r1 + + + + + + SRS18591886 + SAMN36953935 + GSM7707561 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346825 + GSM7707560_r1 + + GSM7707560: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 3, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591885 + GSM7707560 + + + + GSM7707560 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591885 + SAMN36953936 + GSM7707560 + + 5XFAD.Cpa3Cre/+ (MC KO), bio rep 3, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3Cre/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591885 + SAMN36953936 + GSM7707560 + + + + + + + SRR25619899 + GSM7707560_r1 + + + + GSM7707560_r1 + + + + + + SRS18591885 + SAMN36953936 + GSM7707560 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346824 + GSM7707559_r1 + + GSM7707559: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 2, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591884 + GSM7707559 + + + + GSM7707559 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591884 + SAMN36953937 + GSM7707559 + + 5XFAD.Cpa3Cre/+ (MC KO), bio rep 2, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3Cre/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591884 + SAMN36953937 + GSM7707559 + + + + + + + SRR25619900 + GSM7707559_r1 + + + + GSM7707559_r1 + + + + + + SRS18591884 + SAMN36953937 + GSM7707559 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346823 + GSM7707558_r1 + + GSM7707558: 5XFAD.Cpa3+/+ (MC WT), bio rep 2, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591883 + GSM7707558 + + + + GSM7707558 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591883 + SAMN36953938 + GSM7707558 + + 5XFAD.Cpa3+/+ (MC WT), bio rep 2, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3+/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591883 + SAMN36953938 + GSM7707558 + + + + + + + SRR25619901 + GSM7707558_r1 + + + + GSM7707558_r1 + + + + + + SRS18591883 + SAMN36953938 + GSM7707558 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346822 + GSM7707557_r1 + + GSM7707557: 5XFAD.Cpa3Cre/+ (MC KO), bio rep 1, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591882 + GSM7707557 + + + + GSM7707557 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591882 + SAMN36953939 + GSM7707557 + + 5XFAD.Cpa3Cre/+ (MC KO), bio rep 1, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3Cre/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591882 + SAMN36953939 + GSM7707557 + + + + + + + SRR25619902 + GSM7707557_r1 + + + + GSM7707557_r1 + + + + + + SRS18591882 + SAMN36953939 + GSM7707557 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21346821 + GSM7707556_r1 + + GSM7707556: 5XFAD.Cpa3+/+ (MC WT), bio rep 1, scRNA-Seq; Mus musculus; RNA-Seq + + + SRP454723 + PRJNA1004616 + + + + + + + SRS18591881 + GSM7707556 + + + + GSM7707556 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The cortical brain tissue from both hemispheres was dissected and placed in 0.66 mg/ml pre-warmed papain/RPMI medium in C-tubes. The tissues were dissociated using a Gentle MACS dissociator for 37 seconds, followed by incubation at 37°C for 15 minutes under rotation. Next, 0.66 mg/ml pre-warmed collagenase D/RPMI medium was added, and the tissues were dissociated again for 31 seconds using the Gentle MACS dissociator. Next, DNase I (Worthington) was added to the final concentration of 125 U/ml, and the mixture was incubated for another 10 minutes at 37°C under rotation. The tissues were then dissociated for 61 seconds using the Gentle MACS dissociator. The cell suspensions were incubated for 15 min at 37°C under rotation. After the final incubation, we mixed the suspension with neutralization buffer (2% FCS and 1 mM EDTA in PBS) and broke down the tissues by pipetting. The cells were filtered and centrifuged at 400 x g for 8 minutes at 4°C. The supernatant was aspirated, and the cells were resuspended in 27% percoll. The cells were centrifuged again at 850 x g for 40 minutes at 4°C with a deceleration of 4, and then washed and lysed for red blood cells. The cell suspension was resuspended in cold FACS buffer without azide and the viable cells were counted before library preparation. Library was performed according to the manufacturer's instructions. + + + + + NextSeq 2000 + + + + + + SRA1691332 + SUB13755921 + + + + Molecular biology, MGH + +
+ 55 Fruit St + Boston + MA + USA +
+ + Kashish + Chetal + + + + + + SRP454723 + PRJNA1004616 + GSE240687 + + + Gene expression profile at single cell level of mouse cortical brain cells + + We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice. Overall design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq. + GSE240687 + + + + + pubmed + 37713312 + + + + + + + SRS18591881 + SAMN36953940 + GSM7707556 + + 5XFAD.Cpa3+/+ (MC WT), bio rep 1, scRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1004616 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + cell type + brain cells + + + genotype + 5XFAD.Cpa3+/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18591881 + SAMN36953940 + GSM7707556 + + + + + + + SRR25619903 + GSM7707556_r1 + + + + GSM7707556_r1 + + + + + + SRS18591881 + SAMN36953940 + GSM7707556 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE241349.xml b/tests/data/GSE241349.xml new file mode 100644 index 0000000..a31f0d4 --- /dev/null +++ b/tests/data/GSE241349.xml @@ -0,0 +1,1264 @@ + + + + + + + SRX21439176 + GSM7727548_r1 + + GSM7727548: LB-M-RE-MI-3; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676118 + GSM7727548 + + + + GSM7727548 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676118 + SAMN37097541 + GSM7727548 + + LB-M-RE-MI-3 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + drug-resistant epileptic memory impairment + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676118 + SAMN37097541 + GSM7727548 + + + + + + + SRR25714944 + GSM7727548_r1 + + + + GSM7727548_r1 + + + + + + SRS18676118 + SAMN37097541 + GSM7727548 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21439175 + GSM7727547_r1 + + GSM7727547: LB-M-RE-MI-2; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676117 + GSM7727547 + + + + GSM7727547 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676117 + SAMN37097542 + GSM7727547 + + LB-M-RE-MI-2 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + drug-resistant epileptic memory impairment + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676117 + SAMN37097542 + GSM7727547 + + + + + + + SRR25714945 + GSM7727547_r1 + + + + GSM7727547_r1 + + + + + + SRS18676117 + SAMN37097542 + GSM7727547 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21439174 + GSM7727546_r1 + + GSM7727546: LB-M-RE-MI-1; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676116 + GSM7727546 + + + + GSM7727546 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676116 + SAMN37097543 + GSM7727546 + + LB-M-RE-MI-1 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + drug-resistant epileptic memory impairment + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676116 + SAMN37097543 + GSM7727546 + + + + + + + SRR25714946 + GSM7727546_r1 + + + + GSM7727546_r1 + + + + + + SRS18676116 + SAMN37097543 + GSM7727546 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21439173 + GSM7727545_r1 + + GSM7727545: LB-M-Cont-3; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676115 + GSM7727545 + + + + GSM7727545 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676115 + SAMN37097544 + GSM7727545 + + LB-M-Cont-3 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + Control + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676115 + SAMN37097544 + GSM7727545 + + + + + + + SRR25714947 + GSM7727545_r1 + + + + GSM7727545_r1 + + + + + + SRS18676115 + SAMN37097544 + GSM7727545 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21439172 + GSM7727544_r1 + + GSM7727544: LB-M-Cont-2; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676113 + GSM7727544 + + + + GSM7727544 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676113 + SAMN37097545 + GSM7727544 + + LB-M-Cont-2 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + Control + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676113 + SAMN37097545 + GSM7727544 + + + + + + + SRR25714948 + GSM7727544_r1 + + + + GSM7727544_r1 + + + + + + SRS18676113 + SAMN37097545 + GSM7727544 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21439171 + GSM7727543_r1 + + GSM7727543: LB-M-Cont-1; Mus musculus; RNA-Seq + + + SRP456212 + PRJNA1007729 + + + + + + + SRS18676114 + GSM7727543 + + + + GSM7727543 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis. The concentration of singlenucleus suspension was adjusted to 3-4ⅹ10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer's instructions (Single Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1696778 + SUB13787420 + + + + Tangdu Hospital + +
+ Xinsi Road No.1 + Xi'an + Shaanxi Province + China +
+ + Liying + Han + + + + + + SRP456212 + PRJNA1007729 + GSE241349 + + + Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment + + In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors. Overall design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue. + GSE241349 + + + + + pubmed + 39635132 + + + + + + + SRS18676114 + SAMN37097546 + GSM7727543 + + LB-M-Cont-1 + + 10090 + Mus musculus + + + + + bioproject + 1007729 + + + + + + + source_name + Bilateral hippocampus + + + group + Control + + + tissue + Bilateral hippocampus + + + Sex + male + + + age + 14 weeks + + + strain + C57BL/6 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18676114 + SAMN37097546 + GSM7727543 + + + + + + + SRR25714949 + GSM7727543_r1 + + + + GSM7727543_r1 + + + + + + SRS18676114 + SAMN37097546 + GSM7727543 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE242271.xml b/tests/data/GSE242271.xml new file mode 100644 index 0000000..8dcbef5 --- /dev/null +++ b/tests/data/GSE242271.xml @@ -0,0 +1,3529 @@ + + + + + + + SRX21633545 + GSM7757587_r1 + + GSM7757587: scOVCA5_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804179 + GSM7757587 + + + + GSM7757587 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804179 + SAMN37279955 + GSM7757587 + + scOVCA5_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + ovarian cancer + + + tissue + ovarian cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804179 + SAMN37279955 + GSM7757587 + + + + + + + SRR25913438 + GSM7757587_r1 + + + + GSM7757587_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=scOVCA5_CD45_S5_L004_R1_001.fastq.gz --read2PairFiles=scOVCA5_CD45_S5_L004_R2_001.fastq.gz --read3PairFiles=scOVCA5_CD45_S5_L004_I1_001.fastq.gz --read4PairFiles=scOVCA5_CD45_S5_L004_I2_001.fastq.gz + + + + + + SRS18804179 + SAMN37279955 + GSM7757587 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633544 + GSM7757586_r1 + + GSM7757586: scOVCA4_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804176 + GSM7757586 + + + + GSM7757586 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804176 + SAMN37279956 + GSM7757586 + + scOVCA4_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + ovarian cancer + + + tissue + ovarian cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804176 + SAMN37279956 + GSM7757586 + + + + + + + SRR25913439 + GSM7757586_r1 + + + + GSM7757586_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA4_CD45_S4_L003_R1_001.fastq.gz --read2PairFiles=scOVCA4_CD45_S4_L003_R2_001.fastq.gz --read3PairFiles=scOVCA4_CD45_S4_L003_I1_001.fastq.gz + + + + + + SRS18804176 + SAMN37279956 + GSM7757586 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25913440 + GSM7757586_r2 + + + + GSM7757586_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA4_CD45_S4_L004_R1_001.fastq.gz --read2PairFiles=scOVCA4_CD45_S4_L004_R2_001.fastq.gz --read3PairFiles=scOVCA4_CD45_S4_L004_I1_001.fastq.gz + + + + + + SRS18804176 + SAMN37279956 + GSM7757586 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633543 + GSM7757585_r1 + + GSM7757585: scOVCA3_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804178 + GSM7757585 + + + + GSM7757585 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804178 + SAMN37279957 + GSM7757585 + + scOVCA3_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + ovarian cancer + + + tissue + ovarian cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804178 + SAMN37279957 + GSM7757585 + + + + + + + SRR25913441 + GSM7757585_r1 + + + + GSM7757585_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA3_CD45_S10_L003_R1_001.fastq.gz --read2PairFiles=scOVCA3_CD45_S10_L003_R2_001.fastq.gz --read3PairFiles=scOVCA3_CD45_S10_L003_I1_001.fastq.gz + + + + + + SRS18804178 + SAMN37279957 + GSM7757585 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25913442 + GSM7757585_r2 + + + + GSM7757585_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA3_CD45_S10_L004_R1_001.fastq.gz --read2PairFiles=scOVCA3_CD45_S10_L004_R2_001.fastq.gz --read3PairFiles=scOVCA3_CD45_S10_L004_I1_001.fastq.gz + + + + + + SRS18804178 + SAMN37279957 + GSM7757585 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633542 + GSM7757584_r1 + + GSM7757584: scOVCA2_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804177 + GSM7757584 + + + + GSM7757584 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804177 + SAMN37279958 + GSM7757584 + + scOVCA2_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + ovarian cancer + + + tissue + ovarian cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804177 + SAMN37279958 + GSM7757584 + + + + + + + SRR25913443 + GSM7757584_r1 + + + + GSM7757584_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA2_CD45_S2_L003_R1_001.fastq.gz --read2PairFiles=scOVCA2_CD45_S2_L003_R2_001.fastq.gz --read3PairFiles=scOVCA2_CD45_S2_L003_I1_001.fastq.gz + + + + + + SRS18804177 + SAMN37279958 + GSM7757584 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25913444 + GSM7757584_r2 + + + + GSM7757584_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scOVCA2_CD45_S2_L004_R1_001.fastq.gz --read2PairFiles=scOVCA2_CD45_S2_L004_R2_001.fastq.gz --read3PairFiles=scOVCA2_CD45_S2_L004_I1_001.fastq.gz + + + + + + SRS18804177 + SAMN37279958 + GSM7757584 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633541 + GSM7757583_r1 + + GSM7757583: scOVCA1_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804175 + GSM7757583 + + + + GSM7757583 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804175 + SAMN37279959 + GSM7757583 + + scOVCA1_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + ovarian cancer + + + tissue + ovarian cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804175 + SAMN37279959 + GSM7757583 + + + + + + + SRR25913445 + GSM7757583_r1 + + + + GSM7757583_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=5_OVCA1_CD45_S6_L004_R1_001.fastq.gz --read2PairFiles=5_OVCA1_CD45_S6_L004_R2_001.fastq.gz --read3PairFiles=5_OVCA1_CD45_S6_L004_I1_001.fastq.gz + + + + + + SRS18804175 + SAMN37279959 + GSM7757583 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633540 + GSM7757582_r1 + + GSM7757582: scCRC5_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804174 + GSM7757582 + + + + GSM7757582 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804174 + SAMN37279960 + GSM7757582 + + scCRC5_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + colorectal cancer + + + tissue + colorectal cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804174 + SAMN37279960 + GSM7757582 + + + + + + + SRR25913446 + GSM7757582_r1 + + + + GSM7757582_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=CRC9_CD45_S2_L004_R1_001.fastq.gz --read2PairFiles=CRC9_CD45_S2_L004_R2_001.fastq.gz --read3PairFiles=CRC9_CD45_S2_L004_I1_001.fastq.gz --read4PairFiles=CRC9_CD45_S2_L004_I2_001.fastq.gz + + + + + + SRS18804174 + SAMN37279960 + GSM7757582 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633539 + GSM7757581_r1 + + GSM7757581: scCRC4_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804173 + GSM7757581 + + + + GSM7757581 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804173 + SAMN37279961 + GSM7757581 + + scCRC4_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + colorectal cancer + + + tissue + colorectal cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804173 + SAMN37279961 + GSM7757581 + + + + + + + SRR25913447 + GSM7757581_r1 + + + + GSM7757581_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=CRC8_CD45_S4_L004_R1_001.fastq.gz --read2PairFiles=CRC8_CD45_S4_L004_R2_001.fastq.gz --read3PairFiles=CRC8_CD45_S4_L004_I1_001.fastq.gz --read4PairFiles=CRC8_CD45_S4_L004_I2_001.fastq.gz + + + + + + SRS18804173 + SAMN37279961 + GSM7757581 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633538 + GSM7757580_r1 + + GSM7757580: scCRC3_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804170 + GSM7757580 + + + + GSM7757580 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804170 + SAMN37279962 + GSM7757580 + + scCRC3_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + colorectal cancer + + + tissue + colorectal cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804170 + SAMN37279962 + GSM7757580 + + + + + + + SRR25913448 + GSM7757580_r1 + + + + GSM7757580_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CRC7_CD45_S7_L003_R1_001.fastq.gz --read2PairFiles=CRC7_CD45_S7_L003_R2_001.fastq.gz --read3PairFiles=CRC7_CD45_S7_L003_I1_001.fastq.gz + + + + + + SRS18804170 + SAMN37279962 + GSM7757580 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25913449 + GSM7757580_r2 + + + + GSM7757580_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=CRC7_CD45_S7_L004_R1_001.fastq.gz --read2PairFiles=CRC7_CD45_S7_L004_R2_001.fastq.gz --read3PairFiles=CRC7_CD45_S7_L004_I1_001.fastq.gz + + + + + + SRS18804170 + SAMN37279962 + GSM7757580 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633537 + GSM7757579_r1 + + GSM7757579: scCRC2_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804168 + GSM7757579 + + + + GSM7757579 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804168 + SAMN37279963 + GSM7757579 + + scCRC2_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + colorectal cancer + + + tissue + colorectal cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804168 + SAMN37279963 + GSM7757579 + + + + + + + SRR25913450 + GSM7757579_r1 + + + + GSM7757579_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=4_CRC5_CD45_S4_L004_R1_001.fastq.gz --read2PairFiles=4_CRC5_CD45_S4_L004_R2_001.fastq.gz --read3PairFiles=4_CRC5_CD45_S4_L004_I1_001.fastq.gz + + + + + + SRS18804168 + SAMN37279963 + GSM7757579 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633536 + GSM7757578_r1 + + GSM7757578: scCRC1_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804167 + GSM7757578 + + + + GSM7757578 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804167 + SAMN37279964 + GSM7757578 + + scCRC1_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + colorectal cancer + + + tissue + colorectal cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804167 + SAMN37279964 + GSM7757578 + + + + + + + SRR25913451 + GSM7757578_r1 + + + + GSM7757578_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=1_CRC1_CD45_S5_L004_R1_001.fastq.gz --read2PairFiles=1_CRC1_CD45_S5_L004_R2_001.fastq.gz --read3PairFiles=1_CRC1_CD45_S5_L004_I1_001.fastq.gz + + + + + + SRS18804167 + SAMN37279964 + GSM7757578 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633535 + GSM7757577_r1 + + GSM7757577: scBRCA6_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804172 + GSM7757577 + + + + GSM7757577 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804172 + SAMN37279965 + GSM7757577 + + scBRCA6_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + breast cancer + + + tissue + breast cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804172 + SAMN37279965 + GSM7757577 + + + + + + + SRR25913452 + GSM7757577_r1 + + + + GSM7757577_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=scBRCA6_CD45_S1_L004_R1_001.fastq.gz --read2PairFiles=scBRCA6_CD45_S1_L004_R2_001.fastq.gz --read3PairFiles=scBRCA6_CD45_S1_L004_I1_001.fastq.gz --read4PairFiles=scBRCA6_CD45_S1_L004_I2_001.fastq.gz + + + + + + SRS18804172 + SAMN37279965 + GSM7757577 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633534 + GSM7757576_r1 + + GSM7757576: scBRCA5_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804171 + GSM7757576 + + + + GSM7757576 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804171 + SAMN37279966 + GSM7757576 + + scBRCA5_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + breast cancer + + + tissue + breast cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804171 + SAMN37279966 + GSM7757576 + + + + + + + SRR25913453 + GSM7757576_r1 + + + + GSM7757576_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=scBRCA5_CD45_S4_L004_R1_001.fastq.gz --read2PairFiles=scBRCA5_CD45_S4_L004_R2_001.fastq.gz --read3PairFiles=scBRCA5_CD45_S4_L004_I1_001.fastq.gz --read4PairFiles=scBRCA5_CD45_S4_L004_I2_001.fastq.gz + + + + + + SRS18804171 + SAMN37279966 + GSM7757576 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633533 + GSM7757575_r1 + + GSM7757575: scBRCA4_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804169 + GSM7757575 + + + + GSM7757575 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804169 + SAMN37279967 + GSM7757575 + + scBRCA4_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + breast cancer + + + tissue + breast cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804169 + SAMN37279967 + GSM7757575 + + + + + + + SRR25913454 + GSM7757575_r1 + + + + GSM7757575_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scBRCA4_CD45_S3_L003_R1_001.fastq.gz --read2PairFiles=scBRCA4_CD45_S3_L003_R2_001.fastq.gz --read3PairFiles=scBRCA4_CD45_S3_L003_I1_001.fastq.gz + + + + + + SRS18804169 + SAMN37279967 + GSM7757575 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR25913455 + GSM7757575_r2 + + + + GSM7757575_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=scBRCA4_CD45_S3_L004_R1_001.fastq.gz --read2PairFiles=scBRCA4_CD45_S3_L004_R2_001.fastq.gz --read3PairFiles=scBRCA4_CD45_S3_L004_I1_001.fastq.gz + + + + + + SRS18804169 + SAMN37279967 + GSM7757575 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633532 + GSM7757574_r1 + + GSM7757574: scBRCA3_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804165 + GSM7757574 + + + + GSM7757574 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804165 + SAMN37279968 + GSM7757574 + + scBRCA3_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + breast cancer + + + tissue + breast cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804165 + SAMN37279968 + GSM7757574 + + + + + + + SRR25913456 + GSM7757574_r1 + + + + GSM7757574_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=2_BRCA12_CD45_S1_L004_R1_001.fastq.gz --read2PairFiles=2_BRCA12_CD45_S1_L004_R2_001.fastq.gz --read3PairFiles=2_BRCA12_CD45_S1_L004_I1_001.fastq.gz + + + + + + SRS18804165 + SAMN37279968 + GSM7757574 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX21633531 + GSM7757573_r1 + + GSM7757573: scBRCA1_CD45; Homo sapiens; RNA-Seq + + + SRP458541 + PRJNA1012904 + + + + + + + SRS18804166 + GSM7757573 + + + + GSM7757573 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tumor specimens were dissociated, stained and FACS sorted for FVD- CD45+. Isolated cells were washed with 0.5% BSA/PBS twice subjected to single-cell transcriptomic analysis using Chromium 10X platform scRNA-seq libraries were generated using Chromium 10x 3' v3.1 kit following manufacturer's protocol and sequenced by Illumina NovaSeq6000 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1705591 + SUB13817329 + + + + Narumiya-G, Department of Drug Discovery Medicine, Kyoto University + +
+ Yoshidahonmachi + Kyoto + Kyoto + Japan +
+ + Shuh + Narumiya + + + + + + SRP458541 + PRJNA1012904 + GSE242271 + + + Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq] + + Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathways?in these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor. Overall design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment + GSE242271 + + + + + SRS18804166 + SAMN37279969 + GSM7757573 + + scBRCA1_CD45 + + 9606 + Homo sapiens + + + + + bioproject + 1012904 + + + + + + + source_name + breast cancer + + + tissue + breast cancer + + + cell line + primary cell + + + cell type + CD45+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS18804166 + SAMN37279969 + GSM7757573 + + + + + + + SRR25913457 + GSM7757573_r1 + + + + GSM7757573_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBT --read1PairFiles=3_BRCA1_CD45_S1_L004_R1_001.fastq.gz --read2PairFiles=3_BRCA1_CD45_S1_L004_R2_001.fastq.gz --read3PairFiles=3_BRCA1_CD45_S1_L004_I1_001.fastq.gz + + + + + + SRS18804166 + SAMN37279969 + GSM7757573 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE245339.xml b/tests/data/GSE245339.xml new file mode 100644 index 0000000..7ac3dc5 --- /dev/null +++ b/tests/data/GSE245339.xml @@ -0,0 +1,1276 @@ + + + + + + + SRX22089916 + GSM7840997_r1 + + GSM7840997: CSPα KO3; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156327 + GSM7840997 + + + + GSM7840997 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156327 + SAMN37809702 + GSM7840997 + + CSPα KO3 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + CSPalpha KO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156327 + SAMN37809702 + GSM7840997 + + + + + + + SRR26383232 + GSM7840997_r1 + + + + GSM7840997_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156327 + SAMN37809702 + GSM7840997 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22089915 + GSM7840996_r1 + + GSM7840996: CSPα KO2; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156326 + GSM7840996 + + + + GSM7840996 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156326 + SAMN37809703 + GSM7840996 + + CSPα KO2 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + CSPalpha KO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156326 + SAMN37809703 + GSM7840996 + + + + + + + SRR26383233 + GSM7840996_r1 + + + + GSM7840996_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156326 + SAMN37809703 + GSM7840996 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22089914 + GSM7840995_r1 + + GSM7840995: CSPα KO1; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156325 + GSM7840995 + + + + GSM7840995 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156325 + SAMN37809704 + GSM7840995 + + CSPα KO1 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + CSPalpha KO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156325 + SAMN37809704 + GSM7840995 + + + + + + + SRR26383234 + GSM7840995_r1 + + + + GSM7840995_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156325 + SAMN37809704 + GSM7840995 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22089913 + GSM7840994_r1 + + GSM7840994: WT3; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156324 + GSM7840994 + + + + GSM7840994 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156324 + SAMN37809705 + GSM7840994 + + WT3 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156324 + SAMN37809705 + GSM7840994 + + + + + + + SRR26383235 + GSM7840994_r1 + + + + GSM7840994_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156324 + SAMN37809705 + GSM7840994 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22089912 + GSM7840993_r1 + + GSM7840993: WT2; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156323 + GSM7840993 + + + + GSM7840993 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156323 + SAMN37809706 + GSM7840993 + + WT2 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156323 + SAMN37809706 + GSM7840993 + + + + + + + SRR26383236 + GSM7840993_r1 + + + + GSM7840993_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156323 + SAMN37809706 + GSM7840993 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22089911 + GSM7840992_r1 + + GSM7840992: WT1; Mus musculus; RNA-Seq + + + SRP466291 + PRJNA1027846 + + + + + + + SRS19156322 + GSM7840992 + + + + GSM7840992 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissected mouse cortex from P24 littermate mice were gently Dounce homogenized in 2 ml of ice-cold Nuclei EZ Prep buffer (Sigma, Cat.NUC101-1KT) with a loose pestle, and then with a tight pestle each for 25 times. The resulting homogenate was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. SnRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1731757 + SUB13900874 + + + + Depts. of Neuroscience and Neurology, Yale University + +
+ 295 Congress Avenue, BCMM 154D + New Haven + CT + USA +
+ + Sreeganga + Chandra + + + + + + SRP466291 + PRJNA1027846 + GSE245339 + + + Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance + + Cysteine string protein a (CSPa), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPa knockout (KO) mice and littermate controls. Overall design: Nuclei was isolated from CSPa KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples. + GSE245339 + + + + + pubmed + 37873460 + + + + + + + SRS19156322 + SAMN37809707 + GSM7840992 + + WT1 + + 10090 + Mus musculus + + + + + bioproject + 1027846 + + + + + + + source_name + cortex + + + tissue + cortex + + + cell type + cortical cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19156322 + SAMN37809707 + GSM7840992 + + + + + + + SRR26383237 + GSM7840992_r1 + + + + GSM7840992_r1 + + + + + loader + fastq-load.py + + + + + + SRS19156322 + SAMN37809707 + GSM7840992 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE247070.xml b/tests/data/GSE247070.xml new file mode 100644 index 0000000..9e0a82c --- /dev/null +++ b/tests/data/GSE247070.xml @@ -0,0 +1,4108 @@ + + + + + + + SRX22386076 + GSM7882872_r1 + + GSM7882872: WT_Microglia_mouse2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432234 + GSM7882872 + + + + GSM7882872 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + NextSeq 550 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + WT_Microglia_mouse2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + C57BL/6J + + + age + 32 weeks + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + + + + + + SRR26686276 + GSM7882872_r1 + + + + GSM7882872_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686277 + GSM7882872_r2 + + + + GSM7882872_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686278 + GSM7882872_r3 + + + + GSM7882872_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686279 + GSM7882872_r4 + + + + GSM7882872_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432234 + SAMN38123458 + GSM7882872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386075 + GSM7882871_r1 + + GSM7882871: WT_Microglia_mouse1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432233 + GSM7882871 + + + + GSM7882871 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + NextSeq 550 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + WT_Microglia_mouse1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + C57BL/6J + + + age + 32 weeks + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + + + + + + SRR26686280 + GSM7882871_r1 + + + + GSM7882871_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686281 + GSM7882871_r2 + + + + GSM7882871_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686282 + GSM7882871_r3 + + + + GSM7882871_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686283 + GSM7882871_r4 + + + + GSM7882871_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432233 + SAMN38123459 + GSM7882871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386074 + GSM7882870_r1 + + GSM7882870: PompeKO_Microglia_mouse2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432232 + GSM7882870 + + + + GSM7882870 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + NextSeq 550 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + PompeKO_Microglia_mouse2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + + + + + + SRR26686284 + GSM7882870_r1 + + + + GSM7882870_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686285 + GSM7882870_r2 + + + + GSM7882870_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686286 + GSM7882870_r3 + + + + GSM7882870_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686287 + GSM7882870_r4 + + + + GSM7882870_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432232 + SAMN38123460 + GSM7882870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386073 + GSM7882869_r1 + + GSM7882869: PompeKO_Microglia_mouse1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432231 + GSM7882869 + + + + GSM7882869 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + NextSeq 550 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + PompeKO_Microglia_mouse1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + + + + + + SRR26686288 + GSM7882869_r1 + + + + GSM7882869_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686289 + GSM7882869_r2 + + + + GSM7882869_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686290 + GSM7882869_r3 + + + + GSM7882869_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686291 + GSM7882869_r4 + + + + GSM7882869_r1 + + + + + loader + fastq-load.py + + + + + + SRS19432231 + SAMN38123461 + GSM7882869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386072 + GSM7882868_r1 + + GSM7882868: GAAco_mouse1(4517)_microglia_rep2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432230 + GSM7882868 + + + + GSM7882868 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432230 + SAMN38123462 + GSM7882868 + + GAAco_mouse1(4517)_microglia_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432230 + SAMN38123462 + GSM7882868 + + + + + + + SRR26686292 + GSM7882868_r1 + + + + GSM7882868_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Male2sample4517NM_S11_L001_R1_001.fastq.gz --read2PairFiles=D1Male2sample4517NM_S11_L001_R2_001.fastq.gz --read3PairFiles=D1Male2sample4517NM_S11_L001_I1_001.fastq.gz --read4PairFiles=D1Male2sample4517NM_S11_L001_I2_001.fastq.gz + + + + + + SRS19432230 + SAMN38123462 + GSM7882868 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686293 + GSM7882868_r2 + + + + GSM7882868_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Male2sample4517NM_S11_L002_R1_001.fastq.gz --read2PairFiles=D1Male2sample4517NM_S11_L002_R2_001.fastq.gz --read3PairFiles=D1Male2sample4517NM_S11_L002_I1_001.fastq.gz --read4PairFiles=D1Male2sample4517NM_S11_L002_I2_001.fastq.gz + + + + + + SRS19432230 + SAMN38123462 + GSM7882868 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386071 + GSM7882867_r1 + + GSM7882867: GAAco_mouse1(4517)_microglia_rep1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432229 + GSM7882867 + + + + GSM7882867 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432229 + SAMN38123463 + GSM7882867 + + GAAco_mouse1(4517)_microglia_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432229 + SAMN38123463 + GSM7882867 + + + + + + + SRR26686294 + GSM7882867_r1 + + + + GSM7882867_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Male1sample4517M_S9_L001_R1_001.fastq.gz --read2PairFiles=D1Male1sample4517M_S9_L001_R2_001.fastq.gz --read3PairFiles=D1Male1sample4517M_S9_L001_I1_001.fastq.gz --read4PairFiles=D1Male1sample4517M_S9_L001_I2_001.fastq.gz + + + + + + SRS19432229 + SAMN38123463 + GSM7882867 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686295 + GSM7882867_r2 + + + + GSM7882867_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Male1sample4517M_S9_L002_R1_001.fastq.gz --read2PairFiles=D1Male1sample4517M_S9_L002_R2_001.fastq.gz --read3PairFiles=D1Male1sample4517M_S9_L002_I1_001.fastq.gz --read4PairFiles=D1Male1sample4517M_S9_L002_I2_001.fastq.gz + + + + + + SRS19432229 + SAMN38123463 + GSM7882867 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386070 + GSM7882866_r1 + + GSM7882866: GAAco_mouse2(4519)_microglia_rep2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432228 + GSM7882866 + + + + GSM7882866 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432228 + SAMN38123464 + GSM7882866 + + GAAco_mouse2(4519)_microglia_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432228 + SAMN38123464 + GSM7882866 + + + + + + + SRR26686296 + GSM7882866_r1 + + + + GSM7882866_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Female2sample4519NM_S15_L001_R1_001.fastq.gz --read2PairFiles=D1Female2sample4519NM_S15_L001_R2_001.fastq.gz --read3PairFiles=D1Female2sample4519NM_S15_L001_I1_001.fastq.gz --read4PairFiles=D1Female2sample4519NM_S15_L001_I2_001.fastq.gz + + + + + + SRS19432228 + SAMN38123464 + GSM7882866 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686297 + GSM7882866_r2 + + + + GSM7882866_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Female2sample4519NM_S15_L002_R1_001.fastq.gz --read2PairFiles=D1Female2sample4519NM_S15_L002_R2_001.fastq.gz --read3PairFiles=D1Female2sample4519NM_S15_L002_I1_001.fastq.gz --read4PairFiles=D1Female2sample4519NM_S15_L002_I2_001.fastq.gz + + + + + + SRS19432228 + SAMN38123464 + GSM7882866 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386069 + GSM7882865_r1 + + GSM7882865: GAAco_mouse2(4519)_microglia_rep1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432227 + GSM7882865 + + + + GSM7882865 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432227 + SAMN38123465 + GSM7882865 + + GAAco_mouse2(4519)_microglia_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432227 + SAMN38123465 + GSM7882865 + + + + + + + SRR26686298 + GSM7882865_r1 + + + + GSM7882865_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Female1sample4519M_S13_L001_R1_001.fastq.gz --read2PairFiles=D1Female1sample4519M_S13_L001_R2_001.fastq.gz --read3PairFiles=D1Female1sample4519M_S13_L001_I1_001.fastq.gz --read4PairFiles=D1Female1sample4519M_S13_L001_I2_001.fastq.gz + + + + + + SRS19432227 + SAMN38123465 + GSM7882865 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686299 + GSM7882865_r2 + + + + GSM7882865_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D1Female1sample4519M_S13_L002_R1_001.fastq.gz --read2PairFiles=D1Female1sample4519M_S13_L002_R2_001.fastq.gz --read3PairFiles=D1Female1sample4519M_S13_L002_I1_001.fastq.gz --read4PairFiles=D1Female1sample4519M_S13_L002_I2_001.fastq.gz + + + + + + SRS19432227 + SAMN38123465 + GSM7882865 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386068 + GSM7882864_r1 + + GSM7882864: GILT_mouse1(3535)_microglia_rep2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432226 + GSM7882864 + + + + GSM7882864 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432226 + SAMN38123466 + GSM7882864 + + GILT_mouse1(3535)_microglia_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432226 + SAMN38123466 + GSM7882864 + + + + + + + SRR26686300 + GSM7882864_r1 + + + + GSM7882864_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Male2sample3535NM_S3_L001_R1_001.fastq.gz --read2PairFiles=D0Male2sample3535NM_S3_L001_R2_001.fastq.gz --read3PairFiles=D0Male2sample3535NM_S3_L001_I1_001.fastq.gz --read4PairFiles=D0Male2sample3535NM_S3_L001_I2_001.fastq.gz + + + + + + SRS19432226 + SAMN38123466 + GSM7882864 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686301 + GSM7882864_r2 + + + + GSM7882864_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Male2sample3535NM_S3_L002_R1_001.fastq.gz --read2PairFiles=D0Male2sample3535NM_S3_L002_R2_001.fastq.gz --read3PairFiles=D0Male2sample3535NM_S3_L002_I1_001.fastq.gz --read4PairFiles=D0Male2sample3535NM_S3_L002_I2_001.fastq.gz + + + + + + SRS19432226 + SAMN38123466 + GSM7882864 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386067 + GSM7882863_r1 + + GSM7882863: GILT_mouse1(3535)_microglia_rep1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432225 + GSM7882863 + + + + GSM7882863 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432225 + SAMN38123467 + GSM7882863 + + GILT_mouse1(3535)_microglia_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432225 + SAMN38123467 + GSM7882863 + + + + + + + SRR26686302 + GSM7882863_r1 + + + + GSM7882863_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Male1sample3535M_S1_L001_R1_001.fastq.gz --read2PairFiles=D0Male1sample3535M_S1_L001_R2_001.fastq.gz --read3PairFiles=D0Male1sample3535M_S1_L001_I1_001.fastq.gz --read4PairFiles=D0Male1sample3535M_S1_L001_I2_001.fastq.gz + + + + + + SRS19432225 + SAMN38123467 + GSM7882863 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686303 + GSM7882863_r2 + + + + GSM7882863_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Male1sample3535M_S1_L002_R1_001.fastq.gz --read2PairFiles=D0Male1sample3535M_S1_L002_R2_001.fastq.gz --read3PairFiles=D0Male1sample3535M_S1_L002_I1_001.fastq.gz --read4PairFiles=D0Male1sample3535M_S1_L002_I2_001.fastq.gz + + + + + + SRS19432225 + SAMN38123467 + GSM7882863 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386066 + GSM7882862_r1 + + GSM7882862: GILT_mouse2(3536)_microglia_rep2; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432224 + GSM7882862 + + + + GSM7882862 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432224 + SAMN38123468 + GSM7882862 + + GILT_mouse2(3536)_microglia_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432224 + SAMN38123468 + GSM7882862 + + + + + + + SRR26686304 + GSM7882862_r1 + + + + GSM7882862_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Female2sample3536NM_S7_L001_R1_001.fastq.gz --read2PairFiles=D0Female2sample3536NM_S7_L001_R2_001.fastq.gz --read3PairFiles=D0Female2sample3536NM_S7_L001_I1_001.fastq.gz --read4PairFiles=D0Female2sample3536NM_S7_L001_I2_001.fastq.gz + + + + + + SRS19432224 + SAMN38123468 + GSM7882862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686305 + GSM7882862_r2 + + + + GSM7882862_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Female2sample3536NM_S7_L002_R1_001.fastq.gz --read2PairFiles=D0Female2sample3536NM_S7_L002_R2_001.fastq.gz --read3PairFiles=D0Female2sample3536NM_S7_L002_I1_001.fastq.gz --read4PairFiles=D0Female2sample3536NM_S7_L002_I2_001.fastq.gz + + + + + + SRS19432224 + SAMN38123468 + GSM7882862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22386065 + GSM7882861_r1 + + GSM7882861: GILT_mouse2(3536)_microglia_rep1; Mus musculus; RNA-Seq + + + SRP470428 + PRJNA1036162 + + + + + + + SRS19432223 + GSM7882861 + + + + GSM7882861 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology). For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1747766 + SUB13962096 + + + + UCL + +
+ Gower St + London + United Kingdom +
+ + Nazif + Alic + + + + + + SRP470428 + PRJNA1036162 + GSE247070 + + + Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations. + + Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. Overall design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group). + GSE247070 + + + + + SRS19432223 + SAMN38123469 + GSM7882861 + + GILT_mouse2(3536)_microglia_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1036162 + + + + + + + source_name + Brain + + + cell type + Microglia + + + tissue + Brain + + + strain + Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice) + + + age + 32 weeks + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19432223 + SAMN38123469 + GSM7882861 + + + + + + + SRR26686306 + GSM7882861_r1 + + + + GSM7882861_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Female1sample3536M_S5_L001_R1_001.fastq.gz --read2PairFiles=D0Female1sample3536M_S5_L001_R2_001.fastq.gz --read3PairFiles=D0Female1sample3536M_S5_L001_I1_001.fastq.gz --read4PairFiles=D0Female1sample3536M_S5_L001_I2_001.fastq.gz + + + + + + SRS19432223 + SAMN38123469 + GSM7882861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR26686307 + GSM7882861_r2 + + + + GSM7882861_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=D0Female1sample3536M_S5_L002_R1_001.fastq.gz --read2PairFiles=D0Female1sample3536M_S5_L002_R2_001.fastq.gz --read3PairFiles=D0Female1sample3536M_S5_L002_I1_001.fastq.gz --read4PairFiles=D0Female1sample3536M_S5_L002_I2_001.fastq.gz + + + + + + SRS19432223 + SAMN38123469 + GSM7882861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE247695.xml b/tests/data/GSE247695.xml new file mode 100644 index 0000000..01376b0 --- /dev/null +++ b/tests/data/GSE247695.xml @@ -0,0 +1,1692 @@ + + + + + + + SRX22521087 + GSM7898992_r1 + + GSM7898992: P_421_4; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532534 + GSM7898992 + + + + GSM7898992 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532534 + SAMN38249595 + GSM7898992 + + P_421_4 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Ectopic endometrium + + + tissue + Ectopic endometrium + + + condition + peritoneal lesions from ectopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532534 + SAMN38249595 + GSM7898992 + + + + + + + SRR26824401 + GSM7898992_r1 + + + + GSM7898992_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532534 + SAMN38249595 + GSM7898992 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521086 + GSM7898991_r1 + + GSM7898991: P_398_4; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532533 + GSM7898991 + + + + GSM7898991 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532533 + SAMN38249596 + GSM7898991 + + P_398_4 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Ectopic endometrium + + + tissue + Ectopic endometrium + + + condition + peritoneal lesions from ectopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532533 + SAMN38249596 + GSM7898991 + + + + + + + SRR26824402 + GSM7898991_r1 + + + + GSM7898991_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532533 + SAMN38249596 + GSM7898991 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521085 + GSM7898990_r1 + + GSM7898990: P_432_5; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532532 + GSM7898990 + + + + GSM7898990 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532532 + SAMN38249597 + GSM7898990 + + P_432_5 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Ectopic endometrium + + + tissue + Ectopic endometrium + + + condition + peritoneal lesions from ectopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532532 + SAMN38249597 + GSM7898990 + + + + + + + SRR26824403 + GSM7898990_r1 + + + + GSM7898990_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532532 + SAMN38249597 + GSM7898990 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521084 + GSM7898989_r1 + + GSM7898989: P_002_4; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532529 + GSM7898989 + + + + GSM7898989 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532529 + SAMN38249598 + GSM7898989 + + P_002_4 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Ectopic endometrium + + + tissue + Ectopic endometrium + + + condition + peritoneal lesions from ectopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532529 + SAMN38249598 + GSM7898989 + + + + + + + SRR26824404 + GSM7898989_r1 + + + + GSM7898989_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532529 + SAMN38249598 + GSM7898989 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521083 + GSM7898988_r1 + + GSM7898988: E_432_1; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532528 + GSM7898988 + + + + GSM7898988 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532528 + SAMN38249599 + GSM7898988 + + E_432_1 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Eutopic endometrium + + + tissue + Eutopic endometrium + + + condition + eutopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532528 + SAMN38249599 + GSM7898988 + + + + + + + SRR26824405 + GSM7898988_r1 + + + + GSM7898988_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532528 + SAMN38249599 + GSM7898988 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521082 + GSM7898987_r1 + + GSM7898987: E_421_1; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532531 + GSM7898987 + + + + GSM7898987 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532531 + SAMN38249600 + GSM7898987 + + E_421_1 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Eutopic endometrium + + + tissue + Eutopic endometrium + + + condition + eutopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532531 + SAMN38249600 + GSM7898987 + + + + + + + SRR26824406 + GSM7898987_r1 + + + + GSM7898987_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532531 + SAMN38249600 + GSM7898987 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521081 + GSM7898986_r1 + + GSM7898986: E_398_1; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532530 + GSM7898986 + + + + GSM7898986 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532530 + SAMN38249601 + GSM7898986 + + E_398_1 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Eutopic endometrium + + + tissue + Eutopic endometrium + + + condition + eutopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532530 + SAMN38249601 + GSM7898986 + + + + + + + SRR26824407 + GSM7898986_r1 + + + + GSM7898986_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532530 + SAMN38249601 + GSM7898986 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22521080 + GSM7898985_r1 + + GSM7898985: E_002_1; Homo sapiens; RNA-Seq + + + SRP471781 + PRJNA1040179 + + + + + + + SRS19532527 + GSM7898985 + + + + GSM7898985 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1750836 + SUB13972577 + + + + Dept. of Obstetrics and gynecology, University of Tartu + +
+ puusepa8 + tartu + Estonia +
+ + Maire + Peters + + + + + + SRP471781 + PRJNA1040179 + GSE247695 + + + Endometriotic lesions exert distinct metabolic activity compared to paired eutopic endometrium at a single-cell level + + Eutopic endometrium (EuE) and endometriotic peritoneal lesions (ectopic endometrium, EcE) are heterogenous tissues according to the recent scRNA studies. We aimed to explore metabolic profile of cell populations in paired samples of EuE and EcE from four women with endometriosis. We found changes in the regulation of progesterone and estradiol signaling pathways in perivascular, stromal and endothelial cells of EcE compared to EuE, which might have a direct effect on cellular metabolism and contribute to cell proliferation and angiogenesis. The metabolic pathways were differentially regulated in perivascular, stromal and endothelial clusters, and metabolic pathway activity change between EcE and EuE was the highest for AMPK, HIF-1, glutathione metabolism, OXPHOS, and glycolysis/ gluconeogenesis. Remarkably, we identified co-activation of glycolysis and OXPHOS in perivascular and stromal cells of EcE compared to EuE. Previous studies reported a Warburg-like effect in endometriosis with a high use of glycolysis pathway over oxidative metabolism. Our observations might suggest the employment of both OXPHOS and glycolysis to meet the energy demands of proliferating cells in endometriotic lesions. Overall design: Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%. ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3' reagent v3.1 kit. Barcoded full-length cDNAs were produced, and pair-end sequenced targeting 35000 reads per cell using Novaseq PE150. + GSE247695 + + + + + pubmed + 39169201 + + + + + + + SRS19532527 + SAMN38249602 + GSM7898985 + + E_002_1 + + 9606 + Homo sapiens + + + + + bioproject + 1040179 + + + + + + + source_name + Eutopic endometrium + + + tissue + Eutopic endometrium + + + condition + eutopic endometrium + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19532527 + SAMN38249602 + GSM7898985 + + + + + + + SRR26824408 + GSM7898985_r1 + + + + GSM7898985_r1 + + + + + loader + fastq-load.py + + + + + + SRS19532527 + SAMN38249602 + GSM7898985 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE247963.xml b/tests/data/GSE247963.xml new file mode 100644 index 0000000..eb97c03 --- /dev/null +++ b/tests/data/GSE247963.xml @@ -0,0 +1,832 @@ + + + + + + + SRX22544995 + GSM7903862_r1 + + GSM7903862: brian, snRNAseq, PID15_Ctrl; Mus musculus; RNA-Seq + + + SRP472356 + PRJNA1041312 + + + + + + + SRS19554375 + GSM7903862 + + + + GSM7903862 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mouse brain of our bAVM model were harvested Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3' library preparation kit (SeekGene, Cat# SO01V3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1752605 + SUB13983654 + + + + Wooping Ge, Chinese Institute for Brain Research, Beijing(CIBR) + +
+ Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District + Beijing + China +
+ + Xing-jun + Chen + + + + + + SRP472356 + PRJNA1041312 + GSE247963 + + + rAAV-miniBEND: A Targeted Vector for Brain Endothelial Cell Gene Delivery and Cerebrovascular Malformation Modeling + + In-depth analysis of the molecular mechanisms underlying the initiation and development of bAVM was conducted through single-nucleus RNA sequencing of cells from bAVM lesions in Braf-CAfl/fl mice locally injected with AAV-miniBEND. Overall design: Differential expression analysis and Gene Set Enrichment Analysis of single-nucleus RNA sequencing data. We performed differential expression analysis of RNA seq data and Gene Set Enrichment Analysis obtained from bAVM lesions in Braf-CAfl/fl mice and normal brain region samples from the contralateral hemisphere of the same mice served as a control group. + GSE247963 + + + + + SRS19554375 + SAMN38282717 + GSM7903862 + + brian, snRNAseq, PID15_Ctrl + + 10090 + Mus musculus + + + + + bioproject + 1041312 + + + + + + + source_name + brian + + + tissue + brian + + + cell type + endothelial cells + + + group + Ctrl + + + genotype + Braf-CAfl/fl + + + agent + inject with AAV-miniBEND + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19554375 + SAMN38282717 + GSM7903862 + + + + + + + SRR26849506 + GSM7903862_r1 + + + + GSM7903862_r1 + + + + + loader + fastq-load.py + + + + + + SRS19554375 + SAMN38282717 + GSM7903862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22544994 + GSM7903861_r1 + + GSM7903861: brian, snRNAseq, PID15_bAVM; Mus musculus; RNA-Seq + + + SRP472356 + PRJNA1041312 + + + + + + + SRS19554374 + GSM7903861 + + + + GSM7903861 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mouse brain of our bAVM model were harvested Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3' library preparation kit (SeekGene, Cat# SO01V3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1752605 + SUB13983654 + + + + Wooping Ge, Chinese Institute for Brain Research, Beijing(CIBR) + +
+ Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District + Beijing + China +
+ + Xing-jun + Chen + + + + + + SRP472356 + PRJNA1041312 + GSE247963 + + + rAAV-miniBEND: A Targeted Vector for Brain Endothelial Cell Gene Delivery and Cerebrovascular Malformation Modeling + + In-depth analysis of the molecular mechanisms underlying the initiation and development of bAVM was conducted through single-nucleus RNA sequencing of cells from bAVM lesions in Braf-CAfl/fl mice locally injected with AAV-miniBEND. Overall design: Differential expression analysis and Gene Set Enrichment Analysis of single-nucleus RNA sequencing data. We performed differential expression analysis of RNA seq data and Gene Set Enrichment Analysis obtained from bAVM lesions in Braf-CAfl/fl mice and normal brain region samples from the contralateral hemisphere of the same mice served as a control group. + GSE247963 + + + + + SRS19554374 + SAMN38282718 + GSM7903861 + + brian, snRNAseq, PID15_bAVM + + 10090 + Mus musculus + + + + + bioproject + 1041312 + + + + + + + source_name + brian + + + tissue + brian + + + cell type + endothelial cells + + + group + bAVM + + + genotype + Braf-CAfl/fl + + + agent + inject with AAV-miniBEND + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19554374 + SAMN38282718 + GSM7903861 + + + + + + + SRR26849507 + GSM7903861_r1 + + + + GSM7903861_r1 + + + + + loader + fastq-load.py + + + + + + SRS19554374 + SAMN38282718 + GSM7903861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22544993 + GSM7903860_r1 + + GSM7903860: brian, snRNAseq, PID27_Ctrl; Mus musculus; RNA-Seq + + + SRP472356 + PRJNA1041312 + + + + + + + SRS19554373 + GSM7903860 + + + + GSM7903860 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mouse brain of our bAVM model were harvested Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3' library preparation kit (SeekGene, Cat# SO01V3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1752605 + SUB13983654 + + + + Wooping Ge, Chinese Institute for Brain Research, Beijing(CIBR) + +
+ Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District + Beijing + China +
+ + Xing-jun + Chen + + + + + + SRP472356 + PRJNA1041312 + GSE247963 + + + rAAV-miniBEND: A Targeted Vector for Brain Endothelial Cell Gene Delivery and Cerebrovascular Malformation Modeling + + In-depth analysis of the molecular mechanisms underlying the initiation and development of bAVM was conducted through single-nucleus RNA sequencing of cells from bAVM lesions in Braf-CAfl/fl mice locally injected with AAV-miniBEND. Overall design: Differential expression analysis and Gene Set Enrichment Analysis of single-nucleus RNA sequencing data. We performed differential expression analysis of RNA seq data and Gene Set Enrichment Analysis obtained from bAVM lesions in Braf-CAfl/fl mice and normal brain region samples from the contralateral hemisphere of the same mice served as a control group. + GSE247963 + + + + + SRS19554373 + SAMN38282719 + GSM7903860 + + brian, snRNAseq, PID27_Ctrl + + 10090 + Mus musculus + + + + + bioproject + 1041312 + + + + + + + source_name + brian + + + tissue + brian + + + cell type + endothelial cells + + + group + Ctrl + + + genotype + Braf-CAfl/fl + + + agent + inject with AAV-miniBEND + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19554373 + SAMN38282719 + GSM7903860 + + + + + + + SRR26849508 + GSM7903860_r1 + + + + GSM7903860_r1 + + + + + loader + fastq-load.py + + + + + + SRS19554373 + SAMN38282719 + GSM7903860 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22544992 + GSM7903859_r1 + + GSM7903859: brian, snRNAseq, PID27_bAVM; Mus musculus; RNA-Seq + + + SRP472356 + PRJNA1041312 + + + + + + + SRS19554372 + GSM7903859 + + + + GSM7903859 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mouse brain of our bAVM model were harvested Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3' library preparation kit (SeekGene, Cat# SO01V3.1) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1752605 + SUB13983654 + + + + Wooping Ge, Chinese Institute for Brain Research, Beijing(CIBR) + +
+ Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District + Beijing + China +
+ + Xing-jun + Chen + + + + + + SRP472356 + PRJNA1041312 + GSE247963 + + + rAAV-miniBEND: A Targeted Vector for Brain Endothelial Cell Gene Delivery and Cerebrovascular Malformation Modeling + + In-depth analysis of the molecular mechanisms underlying the initiation and development of bAVM was conducted through single-nucleus RNA sequencing of cells from bAVM lesions in Braf-CAfl/fl mice locally injected with AAV-miniBEND. Overall design: Differential expression analysis and Gene Set Enrichment Analysis of single-nucleus RNA sequencing data. We performed differential expression analysis of RNA seq data and Gene Set Enrichment Analysis obtained from bAVM lesions in Braf-CAfl/fl mice and normal brain region samples from the contralateral hemisphere of the same mice served as a control group. + GSE247963 + + + + + SRS19554372 + SAMN38282720 + GSM7903859 + + brian, snRNAseq, PID27_bAVM + + 10090 + Mus musculus + + + + + bioproject + 1041312 + + + + + + + source_name + brian + + + tissue + brian + + + cell type + endothelial cells + + + group + bAVM + + + genotype + Braf-CAfl/fl + + + agent + inject with AAV-miniBEND + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19554372 + SAMN38282720 + GSM7903859 + + + + + + + SRR26849509 + GSM7903859_r1 + + + + GSM7903859_r1 + + + + + loader + fastq-load.py + + + + + + SRS19554372 + SAMN38282720 + GSM7903859 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE249268.xml b/tests/data/GSE249268.xml new file mode 100644 index 0000000..fb6b474 --- /dev/null +++ b/tests/data/GSE249268.xml @@ -0,0 +1,9275 @@ + + + + + + + SRX22734323 + GSM7932631_r1 + + GSM7932631: OPC, P720, Male, 6_8; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722868 + GSM7932631 + + + + GSM7932631 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + OPC, P720, Male, 6_8 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P720 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + + + + + + SRR27044604 + GSM7932631_r1 + + + + GSM7932631_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044605 + GSM7932631_r2 + + + + GSM7932631_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044606 + GSM7932631_r3 + + + + GSM7932631_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044607 + GSM7932631_r4 + + + + GSM7932631_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722868 + SAMN38639758 + GSM7932631 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734322 + GSM7932630_r1 + + GSM7932630: OPC, P720, Male, 10; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722865 + GSM7932630 + + + + GSM7932630 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722865 + SAMN38639759 + GSM7932630 + + OPC, P720, Male, 10 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P720 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722865 + SAMN38639759 + GSM7932630 + + + + + + + SRR27044608 + GSM7932630_r1 + + + + GSM7932630_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722865 + SAMN38639759 + GSM7932630 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734321 + GSM7932627_r1 + + GSM7932627: OPC, P720, Female, 2; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722866 + GSM7932627 + + + + GSM7932627 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722866 + SAMN38639762 + GSM7932627 + + OPC, P720, Female, 2 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P720 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722866 + SAMN38639762 + GSM7932627 + + + + + + + SRR27044609 + GSM7932627_r1 + + + + GSM7932627_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722866 + SAMN38639762 + GSM7932627 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734320 + GSM7932629_r1 + + GSM7932629: OPC, P720, Female, 9; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722867 + GSM7932629 + + + + GSM7932629 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + OPC, P720, Female, 9 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P720 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + + + + + + SRR27044610 + GSM7932629_r1 + + + + GSM7932629_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044611 + GSM7932629_r2 + + + + GSM7932629_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044612 + GSM7932629_r3 + + + + GSM7932629_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044613 + GSM7932629_r4 + + + + GSM7932629_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722867 + SAMN38639760 + GSM7932629 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734319 + GSM7932628_r1 + + GSM7932628: OPC, P720, Female, 3_16; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722863 + GSM7932628 + + + + GSM7932628 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + OPC, P720, Female, 3_16 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P720 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + + + + + + SRR27044614 + GSM7932628_r1 + + + + GSM7932628_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044615 + GSM7932628_r2 + + + + GSM7932628_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044616 + GSM7932628_r3 + + + + GSM7932628_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044617 + GSM7932628_r4 + + + + GSM7932628_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722863 + SAMN38639761 + GSM7932628 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734318 + GSM7932626_r1 + + GSM7932626: OPC, P360, Male, 8; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722857 + GSM7932626 + + + + GSM7932626 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722857 + SAMN38639763 + GSM7932626 + + OPC, P360, Male, 8 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P360 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722857 + SAMN38639763 + GSM7932626 + + + + + + + SRR27044618 + GSM7932626_r1 + + + + GSM7932626_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722857 + SAMN38639763 + GSM7932626 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR27044620 + GSM7932626_r3 + + + + GSM7932626_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722857 + SAMN38639763 + GSM7932626 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044621 + GSM7932626_r4 + + + + GSM7932626_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722857 + SAMN38639763 + GSM7932626 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734317 + GSM7932625_r1 + + GSM7932625: OPC, P360, Male, 13; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722853 + GSM7932625 + + + + GSM7932625 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722853 + SAMN38639764 + GSM7932625 + + OPC, P360, Male, 13 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P360 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722853 + SAMN38639764 + GSM7932625 + + + + + + + SRR27044622 + GSM7932625_r1 + + + + GSM7932625_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722853 + SAMN38639764 + GSM7932625 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX22734316 + GSM7932623_r1 + + GSM7932623: OPC, P360, Female, 5; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722862 + GSM7932623 + + + + GSM7932623 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722862 + SAMN38639766 + GSM7932623 + + OPC, P360, Female, 5 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P360 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722862 + SAMN38639766 + GSM7932623 + + + + + + + SRR27044626 + GSM7932623_r1 + + + + GSM7932623_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722862 + SAMN38639766 + GSM7932623 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX22734315 + GSM7932622_r1 + + GSM7932622: OPC, P360, Female, 2; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722864 + GSM7932622 + + + + GSM7932622 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722864 + SAMN38639767 + GSM7932622 + + OPC, P360, Female, 2 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P360 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722864 + SAMN38639767 + GSM7932622 + + + + + + + SRR27044630 + GSM7932622_r1 + + + + GSM7932622_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722864 + SAMN38639767 + GSM7932622 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX22734314 + GSM7932621_r1 + + GSM7932621: OPC, P180, Male, 1; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722860 + GSM7932621 + + + + GSM7932621 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722860 + SAMN38639768 + GSM7932621 + + OPC, P180, Male, 1 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P180 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722860 + SAMN38639768 + GSM7932621 + + + + + + + SRR27044636 + GSM7932621_r1 + + + + GSM7932621_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722860 + SAMN38639768 + GSM7932621 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + SRX22734313 + GSM7932624_r1 + + GSM7932624: OPC, P360, Male, 1; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722861 + GSM7932624 + + + + GSM7932624 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722861 + SAMN38639765 + GSM7932624 + + OPC, P360, Male, 1 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P360 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722861 + SAMN38639765 + GSM7932624 + + + + + + + SRR27044640 + GSM7932624_r1 + + + + GSM7932624_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722861 + SAMN38639765 + GSM7932624 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX22734312 + GSM7932620_r1 + + GSM7932620: OPC, P180, Female, 4; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722859 + GSM7932620 + + + + GSM7932620 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
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+ + + + + + + + + + + + + + + + SRX22734311 + GSM7932619_r1 + + GSM7932619: OPC, P180, Female, 3; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722856 + GSM7932619 + + + + GSM7932619 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722856 + SAMN38639770 + GSM7932619 + + OPC, P180, Female, 3 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P180 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722856 + SAMN38639770 + GSM7932619 + + + + + + + SRR27044669 + GSM7932619_r1 + + + + GSM7932619_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722856 + SAMN38639770 + GSM7932619 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
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+ + + + + + + + + + + + + + + + SRX22734309 + GSM7932617_r1 + + GSM7932617: OPC, P30, Male, 4; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722854 + GSM7932617 + + + + GSM7932617 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
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+ + + + + + + + + + + + + + + + SRX22734308 + GSM7932613_r1 + + GSM7932613: OPC, P30, Female, 2; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722852 + GSM7932613 + + + + GSM7932613 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722852 + SAMN38639776 + GSM7932613 + + OPC, P30, Female, 2 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P30 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722852 + SAMN38639776 + GSM7932613 + + + + + + + SRR27044678 + GSM7932613_r1 + + + + GSM7932613_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722852 + SAMN38639776 + GSM7932613 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734307 + GSM7932616_r1 + + GSM7932616: OPC, P30, Male, 17; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722851 + GSM7932616 + + + + GSM7932616 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + OPC, P30, Male, 17 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P30 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + + + + + + SRR27044679 + GSM7932616_r1 + + + + GSM7932616_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044680 + GSM7932616_r2 + + + + GSM7932616_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044681 + GSM7932616_r3 + + + + GSM7932616_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044682 + GSM7932616_r4 + + + + GSM7932616_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722851 + SAMN38639773 + GSM7932616 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734306 + GSM7932615_r1 + + GSM7932615: OPC, P30, Male, 10; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722855 + GSM7932615 + + + + GSM7932615 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + OPC, P30, Male, 10 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P30 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + + + + + + SRR27044683 + GSM7932615_r1 + + + + GSM7932615_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044684 + GSM7932615_r2 + + + + GSM7932615_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044685 + GSM7932615_r3 + + + + GSM7932615_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044686 + GSM7932615_r4 + + + + GSM7932615_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722855 + SAMN38639774 + GSM7932615 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734305 + GSM7932614_r1 + + GSM7932614: OPC, P30, Male, 1; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722850 + GSM7932614 + + + + GSM7932614 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + OPC, P30, Male, 1 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P30 + + + Sex + male + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + + + + + + SRR27044687 + GSM7932614_r1 + + + + GSM7932614_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044688 + GSM7932614_r2 + + + + GSM7932614_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + SRR27044689 + GSM7932614_r3 + + + + GSM7932614_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044690 + GSM7932614_r4 + + + + GSM7932614_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722850 + SAMN38639775 + GSM7932614 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX22734304 + GSM7932612_r1 + + GSM7932612: OPC, P30, Female, 13; Mus musculus; RNA-Seq + + + SRP475673 + PRJNA1048408 + + + + + + + SRS19722849 + GSM7932612 + + + + GSM7932612 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer. 10x Chromium Next GEM Single Cell 3' v3 & v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1762750 + SUB14016937 + + + + Dwight Bergles, Neuroscience, Johns Hopkins University + +
+ 725 North Wolfe St., WBSB 1001 + Baltimore + MD + USA +
+ + Dwight + Bergles + + + + + + SRP475673 + PRJNA1048408 + GSE249268 + + + Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan + + Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1a and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts. Overall design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex + GSE249268 + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + OPC, P30, Female, 13 + + 10090 + Mus musculus + + + + + bioproject + 1048408 + + + + + + + source_name + Cortex + + + tissue + Cortex + + + age + P30 + + + Sex + female + + + genotype + Matn4mEGFP/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + + + + + + SRR27044691 + GSM7932612_r1 + + + + GSM7932612_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044692 + GSM7932612_r2 + + + + GSM7932612_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044693 + GSM7932612_r3 + + + + GSM7932612_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27044694 + GSM7932612_r4 + + + + GSM7932612_r1 + + + + + loader + fastq-load.py + + + + + + SRS19722849 + SAMN38639777 + GSM7932612 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE253640.xml b/tests/data/GSE253640.xml new file mode 100644 index 0000000..f674f1e --- /dev/null +++ b/tests/data/GSE253640.xml @@ -0,0 +1,2272 @@ + + + + + + + SRX23306123 + GSM8024496_r1 + + GSM8024496: CTX_Ift88_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182812 + GSM8024496 + + + + GSM8024496 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182812 + SAMN39488029 + GSM8024496 + + CTX_Ift88_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Brain Cortex + + + tissue + Brain Cortex + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182812 + SAMN39488029 + GSM8024496 + + + + + + + SRR27637928 + GSM8024496_r1 + + + + GSM8024496_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182812 + SAMN39488029 + GSM8024496 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX23306122 + GSM8024495_r1 + + GSM8024495: CB_SmoM2-ARL13B_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182811 + GSM8024495 + + + + GSM8024495 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182811 + SAMN39488030 + GSM8024495 + + CB_SmoM2-ARL13B_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Cerebellum + + + tissue + Cerebellum + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182811 + SAMN39488030 + GSM8024495 + + + + + + + SRR27637929 + GSM8024495_r1 + + + + GSM8024495_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182811 + SAMN39488030 + GSM8024495 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX23306121 + GSM8024494_r1 + + GSM8024494: CTX_SmoM2-ARL13B_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182810 + GSM8024494 + + + + GSM8024494 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182810 + SAMN39488031 + GSM8024494 + + CTX_SmoM2-ARL13B_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Brain Cortex + + + tissue + Brain Cortex + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182810 + SAMN39488031 + GSM8024494 + + + + + + + SRR27637930 + GSM8024494_r1 + + + + GSM8024494_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182810 + SAMN39488031 + GSM8024494 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX23306120 + GSM8024493_r1 + + GSM8024493: CB_Smo_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182809 + GSM8024493 + + + + GSM8024493 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182809 + SAMN39488032 + GSM8024493 + + CB_Smo_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Cerebellum + + + tissue + Cerebellum + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182809 + SAMN39488032 + GSM8024493 + + + + + + + SRR27637931 + GSM8024493_r1 + + + + GSM8024493_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182809 + SAMN39488032 + GSM8024493 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX23306119 + GSM8024492_r1 + + GSM8024492: CTX_Smo_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182807 + GSM8024492 + + + + GSM8024492 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182807 + SAMN39488033 + GSM8024492 + + CTX_Smo_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Brain Cortex + + + tissue + Brain Cortex + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182807 + SAMN39488033 + GSM8024492 + + + + + + + SRR27637932 + GSM8024492_r1 + + + + GSM8024492_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182807 + SAMN39488033 + GSM8024492 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
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+ + + + + + + + + + + + + + + + SRX23306118 + GSM8024491_r1 + + GSM8024491: CB_Arl13b_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182808 + GSM8024491 + + + + GSM8024491 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182808 + SAMN39488034 + GSM8024491 + + CB_Arl13b_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Cerebellum + + + tissue + Cerebellum + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182808 + SAMN39488034 + GSM8024491 + + + + + + + SRR27637933 + GSM8024491_r1 + + + + GSM8024491_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182808 + SAMN39488034 + GSM8024491 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX23306117 + GSM8024490_r1 + + GSM8024490: CTX_Arl13b_cKO; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182806 + GSM8024490 + + + + GSM8024490 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182806 + SAMN39488035 + GSM8024490 + + CTX_Arl13b_cKO + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Brain Cortex + + + tissue + Brain Cortex + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182806 + SAMN39488035 + GSM8024490 + + + + + + + SRR27637934 + GSM8024490_r1 + + + + GSM8024490_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182806 + SAMN39488035 + GSM8024490 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX23306116 + GSM8024489_r1 + + GSM8024489: CB_Control2; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182805 + GSM8024489 + + + + GSM8024489 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182805 + SAMN39488036 + GSM8024489 + + CB_Control2 + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Cerebellum + + + tissue + Cerebellum + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182805 + SAMN39488036 + GSM8024489 + + + + + + + SRR27637935 + GSM8024489_r1 + + + + GSM8024489_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182805 + SAMN39488036 + GSM8024489 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX23306115 + GSM8024488_r1 + + GSM8024488: CB_Control1; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182804 + GSM8024488 + + + + GSM8024488 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182804 + SAMN39488037 + GSM8024488 + + CB_Control1 + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Cerebellum + + + tissue + Cerebellum + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182804 + SAMN39488037 + GSM8024488 + + + + + + + SRR27637936 + GSM8024488_r1 + + + + GSM8024488_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182804 + SAMN39488037 + GSM8024488 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX23306114 + GSM8024487_r1 + + GSM8024487: CTX_Control; Mus musculus; RNA-Seq + + + SRP484584 + PRJNA1066391 + + + + + + + SRS20182803 + GSM8024487 + + + + GSM8024487 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. The PCR amplification steps were run 12x. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1788104 + SUB14160901 + + + + Guo Lab, Cell Biology and Anatomy, University of Calgary + +
+ 2500 University Dr NW + Calgary + Canada +
+ + Jiami + Guo + + + + + + SRP484584 + PRJNA1066391 + GSE253640 + + + Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain + + Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Overall design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3' gene expression kit, version 3.1) and processed according to the manufacturer's protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R. + GSE253640 + + + + + pubmed + 39103557 + + + + + + parent_bioproject + PRJNA1066386 + + + + + + SRS20182803 + SAMN39488038 + GSM8024487 + + CTX_Control + + 10090 + Mus musculus + + + + + bioproject + 1066391 + + + + + + + source_name + Brain Cortex + + + tissue + Brain Cortex + + + age + P52-P55 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20182803 + SAMN39488038 + GSM8024487 + + + + + + + SRR27637937 + GSM8024487_r1 + + + + GSM8024487_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS20182803 + SAMN39488038 + GSM8024487 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE254044.xml b/tests/data/GSE254044.xml new file mode 100644 index 0000000..e9141a2 --- /dev/null +++ b/tests/data/GSE254044.xml @@ -0,0 +1,1700 @@ + + + + + + + SRX23371270 + GSM8032544_r1 + + GSM8032544: PF_MUT_rep2; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233505 + GSM8032544 + + + + GSM8032544 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233505 + SAMN39582618 + GSM8032544 + + PF_MUT_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + paraflocculus/flocculus + + + tissue + paraflocculus/flocculus + + + genotype + Tbx1+/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233505 + SAMN39582618 + GSM8032544 + + + + + + + SRR27704462 + GSM8032544_r1 + + + + GSM8032544_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233505 + SAMN39582618 + GSM8032544 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371269 + GSM8032543_r1 + + GSM8032543: PF_WT_rep2; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233503 + GSM8032543 + + + + GSM8032543 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233503 + SAMN39582619 + GSM8032543 + + PF_WT_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + paraflocculus/flocculus + + + tissue + paraflocculus/flocculus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233503 + SAMN39582619 + GSM8032543 + + + + + + + SRR27704463 + GSM8032543_r1 + + + + GSM8032543_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233503 + SAMN39582619 + GSM8032543 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371268 + GSM8032542_r1 + + GSM8032542: Bone_MUT_rep2; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233502 + GSM8032542 + + + + GSM8032542 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233502 + SAMN39582620 + GSM8032542 + + Bone_MUT_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + petrous bone + + + tissue + petrous bone + + + genotype + Tbx1+/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233502 + SAMN39582620 + GSM8032542 + + + + + + + SRR27704464 + GSM8032542_r1 + + + + GSM8032542_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233502 + SAMN39582620 + GSM8032542 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371267 + GSM8032541_r1 + + GSM8032541: Bone_WT_rep2; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233501 + GSM8032541 + + + + GSM8032541 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233501 + SAMN39582621 + GSM8032541 + + Bone_WT_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + petrous bone + + + tissue + petrous bone + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233501 + SAMN39582621 + GSM8032541 + + + + + + + SRR27704465 + GSM8032541_r1 + + + + GSM8032541_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233501 + SAMN39582621 + GSM8032541 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371266 + GSM8032540_r1 + + GSM8032540: Bone_MUT_rep1; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233499 + GSM8032540 + + + + GSM8032540 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233499 + SAMN39582622 + GSM8032540 + + Bone_MUT_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + petrous bone + + + tissue + petrous bone + + + genotype + Tbx1+/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233499 + SAMN39582622 + GSM8032540 + + + + + + + SRR27704466 + GSM8032540_r1 + + + + GSM8032540_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233499 + SAMN39582622 + GSM8032540 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371265 + GSM8032539_r1 + + GSM8032539: Bone_WT_rep1; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233500 + GSM8032539 + + + + GSM8032539 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233500 + SAMN39582623 + GSM8032539 + + Bone_WT_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + petrous bone + + + tissue + petrous bone + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233500 + SAMN39582623 + GSM8032539 + + + + + + + SRR27704467 + GSM8032539_r1 + + + + GSM8032539_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233500 + SAMN39582623 + GSM8032539 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371264 + GSM8032538_r1 + + GSM8032538: PF_MUT_rep1; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233504 + GSM8032538 + + + + GSM8032538 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233504 + SAMN39582624 + GSM8032538 + + PF_MUT_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + paraflocculus/flocculus + + + tissue + paraflocculus/flocculus + + + genotype + Tbx1+/- + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233504 + SAMN39582624 + GSM8032538 + + + + + + + SRR27704468 + GSM8032538_r1 + + + + GSM8032538_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233504 + SAMN39582624 + GSM8032538 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23371263 + GSM8032537_r1 + + GSM8032537: PF_WT_rep1; Mus musculus; RNA-Seq + + + SRP485524 + PRJNA1068192 + + + + + + + SRS20233498 + GSM8032537 + + + + GSM8032537 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001). Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq snRNA-seq + + + + + NextSeq 500 + + + + + + SRA1790865 + SUB14170618 + + + + Developmental Neurobiology, St. Jude Children's Research Hospital + +
+ 262 Danny Thomas Pl, M2426 + Memphis + Tennessee + USA +
+ + Stanislav + Zakharenko + + + + + + SRP485524 + PRJNA1068192 + GSE254044 + + + Tbx1 haploinsufficiency induces bone-to-cerebellar deformity in 22q11.2 deletion syndrome + + 22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency. Overall design: Transcriptome profiling by snRNA-seq in the developing petrous bone and paraflocculus/flocculus from the wild type and Tbx1+/- mouse at P5.5. The study included five mice in each group, with two replicates per group + GSE254044 + + + + + pubmed + 39638997 + + + + + + + SRS20233498 + SAMN39582625 + GSM8032537 + + PF_WT_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1068192 + + + + + + + source_name + paraflocculus/flocculus + + + tissue + paraflocculus/flocculus + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20233498 + SAMN39582625 + GSM8032537 + + + + + + + SRR27704469 + GSM8032537_r1 + + + + GSM8032537_r1 + + + + + loader + fastq-load.py + + + + + + SRS20233498 + SAMN39582625 + GSM8032537 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE254104.xml b/tests/data/GSE254104.xml new file mode 100644 index 0000000..c9daf86 --- /dev/null +++ b/tests/data/GSE254104.xml @@ -0,0 +1,11703 @@ + + + + + + + SRX25254865 + GSM8386423_r1 + + GSM8386423: LG31E4_R47H_101; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940186 + GSM8386423 + + + + GSM8386423 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + LG31E4_R47H_101 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 10.1m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + SRR29753988 + GSM8386423_r1 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753989 + GSM8386423_r2 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753990 + GSM8386423_r3 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753991 + GSM8386423_r4 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753992 + GSM8386423_r5 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753993 + GSM8386423_r6 + + + + GSM8386423_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940186 + SAMN42385444 + GSM8386423 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25254864 + GSM8386422_r1 + + GSM8386422: LG31E4_R47H_68; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940185 + GSM8386422 + + + + GSM8386422 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + LG31E4_R47H_68 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.8m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + SRR29753994 + GSM8386422_r1 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753995 + GSM8386422_r2 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753996 + GSM8386422_r3 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753997 + GSM8386422_r4 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753998 + GSM8386422_r5 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29753999 + GSM8386422_r6 + + + + GSM8386422_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940185 + SAMN42385445 + GSM8386422 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25254863 + GSM8386421_r1 + + GSM8386421: LG31E4_R47H_32; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940184 + GSM8386421 + + + + GSM8386421 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940184 + SAMN42385446 + GSM8386421 + + LG31E4_R47H_32 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940184 + SAMN42385446 + GSM8386421 + + + + + + + SRR29754000 + GSM8386421_r1 + + + + GSM8386421_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940184 + SAMN42385446 + GSM8386421 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX25254861 + GSM8386419_r1 + + GSM8386419: LG31E4_R47H_61; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940183 + GSM8386419 + + + + GSM8386419 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940183 + SAMN42385448 + GSM8386419 + + LG31E4_R47H_61 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.9m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940183 + SAMN42385448 + GSM8386419 + + + + + + + SRR29754012 + GSM8386419_r1 + + + + GSM8386419_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940183 + SAMN42385448 + GSM8386419 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX25254860 + GSM8386418_r1 + + GSM8386418: LG31E4_R47H_60; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940181 + GSM8386418 + + + + GSM8386418 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940181 + SAMN42385449 + GSM8386418 + + LG31E4_R47H_60 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.9m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940181 + SAMN42385449 + GSM8386418 + + + + + + + SRR29754018 + GSM8386418_r1 + + + + GSM8386418_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940181 + SAMN42385449 + GSM8386418 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX25254859 + GSM8386417_r1 + + GSM8386417: LG31E4_R47H_94; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940180 + GSM8386417 + + + + GSM8386417 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940180 + SAMN42385450 + GSM8386417 + + LG31E4_R47H_94 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.6m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940180 + SAMN42385450 + GSM8386417 + + + + + + + SRR29754024 + GSM8386417_r1 + + + + GSM8386417_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940180 + SAMN42385450 + GSM8386417 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX25254858 + GSM8386416_r1 + + GSM8386416: LG31E4_R47H_80; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940178 + GSM8386416 + + + + GSM8386416 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940178 + SAMN42385451 + GSM8386416 + + LG31E4_R47H_80 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940178 + SAMN42385451 + GSM8386416 + + + + + + + SRR29754030 + GSM8386416_r1 + + + + GSM8386416_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940178 + SAMN42385451 + GSM8386416 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX25254857 + GSM8386415_r1 + + GSM8386415: LG31E4_R47H_78; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS21940179 + GSM8386415 + + + + GSM8386415 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1920317 + SUB14593180 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS21940179 + SAMN42385452 + GSM8386415 + + LG31E4_R47H_78 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + male + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21940179 + SAMN42385452 + GSM8386415 + + + + + + + SRR29754036 + GSM8386415_r1 + + + + GSM8386415_r1 + + + + + loader + fastq-load.py + + + + + + SRS21940179 + SAMN42385452 + GSM8386415 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382478 + GSM8033412_r1 + + GSM8033412: LG31E4_73; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243969 + GSM8033412 + + + + GSM8033412 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243969 + SAMN39598454 + GSM8033412 + + LG31E4_73 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.6m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243969 + SAMN39598454 + GSM8033412 + + + + + + + SRR27716250 + GSM8033412_r1 + + + + GSM8033412_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243969 + SAMN39598454 + GSM8033412 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382477 + GSM8033411_r1 + + GSM8033411: LG31E4_54; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243968 + GSM8033411 + + + + GSM8033411 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243968 + SAMN39598455 + GSM8033411 + + LG31E4_54 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.5m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243968 + SAMN39598455 + GSM8033411 + + + + + + + SRR27716252 + GSM8033411_r1 + + + + GSM8033411_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243968 + SAMN39598455 + GSM8033411 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382476 + GSM8033410_r1 + + GSM8033410: LG31E4_45; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243967 + GSM8033410 + + + + GSM8033410 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243967 + SAMN39598456 + GSM8033410 + + LG31E4_45 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243967 + SAMN39598456 + GSM8033410 + + + + + + + SRR27716254 + GSM8033410_r1 + + + + GSM8033410_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243967 + SAMN39598456 + GSM8033410 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382475 + GSM8033408_r1 + + GSM8033408: LG31E4_33; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243966 + GSM8033408 + + + + GSM8033408 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243966 + SAMN39598458 + GSM8033408 + + LG31E4_33 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.8m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243966 + SAMN39598458 + GSM8033408 + + + + + + + SRR27716256 + GSM8033408_r1 + + + + GSM8033408_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243966 + SAMN39598458 + GSM8033408 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382474 + GSM8033409_r1 + + GSM8033409: LG31E4_44; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243965 + GSM8033409 + + + + GSM8033409 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243965 + SAMN39598457 + GSM8033409 + + LG31E4_44 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243965 + SAMN39598457 + GSM8033409 + + + + + + + SRR27716258 + GSM8033409_r1 + + + + GSM8033409_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243965 + SAMN39598457 + GSM8033409 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382473 + GSM8033407_r1 + + GSM8033407: LG31E4_28; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243964 + GSM8033407 + + + + GSM8033407 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243964 + SAMN39598459 + GSM8033407 + + LG31E4_28 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243964 + SAMN39598459 + GSM8033407 + + + + + + + SRR27716264 + GSM8033407_r1 + + + + GSM8033407_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243964 + SAMN39598459 + GSM8033407 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716265 + GSM8033407_r2 + + + + GSM8033407_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243964 + SAMN39598459 + GSM8033407 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382472 + GSM8033406_r1 + + GSM8033406: LG31E4_27; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243963 + GSM8033406 + + + + GSM8033406 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243963 + SAMN39598460 + GSM8033406 + + LG31E4_27 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243963 + SAMN39598460 + GSM8033406 + + + + + + + SRR27716266 + GSM8033406_r1 + + + + GSM8033406_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243963 + SAMN39598460 + GSM8033406 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716267 + GSM8033406_r2 + + + + GSM8033406_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243963 + SAMN39598460 + GSM8033406 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382471 + GSM8033405_r1 + + GSM8033405: LG31E4_25; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243962 + GSM8033405 + + + + GSM8033405 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243962 + SAMN39598461 + GSM8033405 + + LG31E4_25 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.7m + + + genotype + Human ApoE4: E4/E4; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243962 + SAMN39598461 + GSM8033405 + + + + + + + SRR27716268 + GSM8033405_r1 + + + + GSM8033405_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243962 + SAMN39598461 + GSM8033405 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716269 + GSM8033405_r2 + + + + GSM8033405_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243962 + SAMN39598461 + GSM8033405 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382470 + GSM8033404_r1 + + GSM8033404: LG31E4_22; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243961 + GSM8033404 + + + + GSM8033404 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243961 + SAMN39598462 + GSM8033404 + + LG31E4_22 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 10.1m + + + genotype + Human ApoE4: E4/E4; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243961 + SAMN39598462 + GSM8033404 + + + + + + + SRR27716270 + GSM8033404_r1 + + + + GSM8033404_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243961 + SAMN39598462 + GSM8033404 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382469 + GSM8033403_r1 + + GSM8033403: LG31E3_9; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243960 + GSM8033403 + + + + GSM8033403 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243960 + SAMN39598463 + GSM8033403 + + LG31E3_9 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 13.1m + + + genotype + Human ApoE3: E3/E3; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243960 + SAMN39598463 + GSM8033403 + + + + + + + SRR27716272 + GSM8033403_r1 + + + + GSM8033403_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243960 + SAMN39598463 + GSM8033403 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382468 + GSM8033402_r1 + + GSM8033402: LG31E3_40; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243959 + GSM8033402 + + + + GSM8033402 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243959 + SAMN39598464 + GSM8033402 + + LG31E3_40 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.8m + + + genotype + Human ApoE3: E3/E3; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243959 + SAMN39598464 + GSM8033402 + + + + + + + SRR27716278 + GSM8033402_r1 + + + + GSM8033402_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243959 + SAMN39598464 + GSM8033402 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382467 + GSM8033401_r1 + + GSM8033401: LG31E3_4; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243958 + GSM8033401 + + + + GSM8033401 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243958 + SAMN39598465 + GSM8033401 + + LG31E3_4 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.6m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243958 + SAMN39598465 + GSM8033401 + + + + + + + SRR27716284 + GSM8033401_r1 + + + + GSM8033401_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243958 + SAMN39598465 + GSM8033401 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382466 + GSM8033399_r1 + + GSM8033399: LG31E3_18; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243957 + GSM8033399 + + + + GSM8033399 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243957 + SAMN39598467 + GSM8033399 + + LG31E3_18 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.2m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243957 + SAMN39598467 + GSM8033399 + + + + + + + SRR27716286 + GSM8033399_r1 + + + + GSM8033399_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243957 + SAMN39598467 + GSM8033399 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382465 + GSM8033400_r1 + + GSM8033400: LG31E3_38; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243956 + GSM8033400 + + + + GSM8033400 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243956 + SAMN39598466 + GSM8033400 + + LG31E3_38 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.8m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243956 + SAMN39598466 + GSM8033400 + + + + + + + SRR27716288 + GSM8033400_r1 + + + + GSM8033400_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243956 + SAMN39598466 + GSM8033400 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23382464 + GSM8033398_r1 + + GSM8033398: LG31E3_17; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243955 + GSM8033398 + + + + GSM8033398 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243955 + SAMN39598468 + GSM8033398 + + LG31E3_17 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.2m + + + genotype + Human ApoE3: E3/E3; P301S tau: -; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243955 + SAMN39598468 + GSM8033398 + + + + + + + SRR27716294 + GSM8033398_r1 + + + + GSM8033398_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243955 + SAMN39598468 + GSM8033398 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716295 + GSM8033398_r2 + + + + GSM8033398_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243955 + SAMN39598468 + GSM8033398 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382463 + GSM8033397_r1 + + GSM8033397: LG31E3_12; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243954 + GSM8033397 + + + + GSM8033397 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243954 + SAMN39598469 + GSM8033397 + + LG31E3_12 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.9m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243954 + SAMN39598469 + GSM8033397 + + + + + + + SRR27716296 + GSM8033397_r1 + + + + GSM8033397_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243954 + SAMN39598469 + GSM8033397 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716297 + GSM8033397_r2 + + + + GSM8033397_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243954 + SAMN39598469 + GSM8033397 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382462 + GSM8033396_r1 + + GSM8033396: LG31E3_11; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243953 + GSM8033396 + + + + GSM8033396 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243953 + SAMN39598470 + GSM8033396 + + LG31E3_11 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.9m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/KI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243953 + SAMN39598470 + GSM8033396 + + + + + + + SRR27716298 + GSM8033396_r1 + + + + GSM8033396_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243953 + SAMN39598470 + GSM8033396 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716299 + GSM8033396_r2 + + + + GSM8033396_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243953 + SAMN39598470 + GSM8033396 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23382461 + GSM8033395_r1 + + GSM8033395: LG31E3_1; Mus musculus; RNA-Seq + + + SRP485725 + PRJNA1068567 + + + + + + + SRS20243952 + GSM8033395 + + + + GSM8033395 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1791313 + SUB14171855 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP485725 + PRJNA1068567 + GSE254104 + + + Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq] + + The strongest risk factors for Alzheimer's disease (AD) include the ?4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk. Overall design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3). + GSE254104 + + + + + pubmed + 39353433 + + + + + + + SRS20243952 + SAMN39598471 + GSM8033395 + + LG31E3_1 + + 10090 + Mus musculus + + + + + bioproject + 1068567 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + Sex + female + + + age + 9.6m + + + genotype + Human ApoE3: E3/E3; P301S tau: +; R47H Human TREM2 KI: +/+ + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20243952 + SAMN39598471 + GSM8033395 + + + + + + + SRR27716300 + GSM8033395_r1 + + + + GSM8033395_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243952 + SAMN39598471 + GSM8033395 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR27716301 + GSM8033395_r2 + + + + GSM8033395_r1 + + + + + loader + fastq-load.py + + + + + + SRS20243952 + SAMN39598471 + GSM8033395 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE255460.xml b/tests/data/GSE255460.xml new file mode 100644 index 0000000..9d54ef6 --- /dev/null +++ b/tests/data/GSE255460.xml @@ -0,0 +1,3812 @@ + + + + + + + SRX23585145 + GSM8072852_r1 + + GSM8072852: OA8-2_Condition_WB_Rep8; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430107 + GSM8072852 + + + + GSM8072852 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430107 + SAMN39900221 + GSM8072852 + + OA8-2_Condition_WB_Rep8 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430107 + SAMN39900221 + GSM8072852 + + + + + + + SRR27928089 + GSM8072852_r1 + + + + GSM8072852_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430107 + SAMN39900221 + GSM8072852 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585144 + GSM8072851_r1 + + GSM8072851: OA8-1_Condition_NWB_Rep8; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430108 + GSM8072851 + + + + GSM8072851 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430108 + SAMN39900222 + GSM8072851 + + OA8-1_Condition_NWB_Rep8 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430108 + SAMN39900222 + GSM8072851 + + + + + + + SRR27928090 + GSM8072851_r1 + + + + GSM8072851_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430108 + SAMN39900222 + GSM8072851 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585143 + GSM8072850_r1 + + GSM8072850: OA7-2_Condition_WB_Rep7; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430106 + GSM8072850 + + + + GSM8072850 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430106 + SAMN39900223 + GSM8072850 + + OA7-2_Condition_WB_Rep7 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430106 + SAMN39900223 + GSM8072850 + + + + + + + SRR27928091 + GSM8072850_r1 + + + + GSM8072850_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430106 + SAMN39900223 + GSM8072850 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585142 + GSM8072849_r1 + + GSM8072849: OA7-1_Condition_NWB_Rep7; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430104 + GSM8072849 + + + + GSM8072849 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430104 + SAMN39900224 + GSM8072849 + + OA7-1_Condition_NWB_Rep7 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430104 + SAMN39900224 + GSM8072849 + + + + + + + SRR27928092 + GSM8072849_r1 + + + + GSM8072849_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430104 + SAMN39900224 + GSM8072849 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585141 + GSM8072848_r1 + + GSM8072848: OA6-2_Condition_WB_Rep6; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430103 + GSM8072848 + + + + GSM8072848 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430103 + SAMN39900225 + GSM8072848 + + OA6-2_Condition_WB_Rep6 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430103 + SAMN39900225 + GSM8072848 + + + + + + + SRR27928093 + GSM8072848_r1 + + + + GSM8072848_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430103 + SAMN39900225 + GSM8072848 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585140 + GSM8072847_r1 + + GSM8072847: OA6-1_Condition_NWB_Rep6; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430100 + GSM8072847 + + + + GSM8072847 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430100 + SAMN39900226 + GSM8072847 + + OA6-1_Condition_NWB_Rep6 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430100 + SAMN39900226 + GSM8072847 + + + + + + + SRR27928094 + GSM8072847_r1 + + + + GSM8072847_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430100 + SAMN39900226 + GSM8072847 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585139 + GSM8072846_r1 + + GSM8072846: OA5-2_Condition_WB_Rep5; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430101 + GSM8072846 + + + + GSM8072846 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430101 + SAMN39900227 + GSM8072846 + + OA5-2_Condition_WB_Rep5 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430101 + SAMN39900227 + GSM8072846 + + + + + + + SRR27928095 + GSM8072846_r1 + + + + GSM8072846_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430101 + SAMN39900227 + GSM8072846 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585138 + GSM8072845_r1 + + GSM8072845: OA5-1_Condition_NWB_Rep5; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430097 + GSM8072845 + + + + GSM8072845 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430097 + SAMN39900228 + GSM8072845 + + OA5-1_Condition_NWB_Rep5 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430097 + SAMN39900228 + GSM8072845 + + + + + + + SRR27928096 + GSM8072845_r1 + + + + GSM8072845_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430097 + SAMN39900228 + GSM8072845 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585137 + GSM8072844_r1 + + GSM8072844: OA4-2_Condition_WB_Rep4; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430099 + GSM8072844 + + + + GSM8072844 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430099 + SAMN39900229 + GSM8072844 + + OA4-2_Condition_WB_Rep4 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430099 + SAMN39900229 + GSM8072844 + + + + + + + SRR27928097 + GSM8072844_r1 + + + + GSM8072844_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430099 + SAMN39900229 + GSM8072844 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585136 + GSM8072843_r1 + + GSM8072843: OA4-1_Condition_NWB_Rep4; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430102 + GSM8072843 + + + + GSM8072843 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430102 + SAMN39900230 + GSM8072843 + + OA4-1_Condition_NWB_Rep4 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430102 + SAMN39900230 + GSM8072843 + + + + + + + SRR27928098 + GSM8072843_r1 + + + + GSM8072843_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430102 + SAMN39900230 + GSM8072843 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585135 + GSM8072842_r1 + + GSM8072842: OA3-2_Condition_WB_Rep3; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430098 + GSM8072842 + + + + GSM8072842 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430098 + SAMN39900231 + GSM8072842 + + OA3-2_Condition_WB_Rep3 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430098 + SAMN39900231 + GSM8072842 + + + + + + + SRR27928099 + GSM8072842_r1 + + + + GSM8072842_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430098 + SAMN39900231 + GSM8072842 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585134 + GSM8072841_r1 + + GSM8072841: OA3-1_Condition_NWB_Rep3; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430105 + GSM8072841 + + + + GSM8072841 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430105 + SAMN39900232 + GSM8072841 + + OA3-1_Condition_NWB_Rep3 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430105 + SAMN39900232 + GSM8072841 + + + + + + + SRR27928100 + GSM8072841_r1 + + + + GSM8072841_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430105 + SAMN39900232 + GSM8072841 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585133 + GSM8072840_r1 + + GSM8072840: OA2-2_Condition_WB_Rep2; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430096 + GSM8072840 + + + + GSM8072840 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430096 + SAMN39900233 + GSM8072840 + + OA2-2_Condition_WB_Rep2 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430096 + SAMN39900233 + GSM8072840 + + + + + + + SRR27928101 + GSM8072840_r1 + + + + GSM8072840_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430096 + SAMN39900233 + GSM8072840 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585132 + GSM8072839_r1 + + GSM8072839: OA2-1_Condition_NWB_Rep2; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430093 + GSM8072839 + + + + GSM8072839 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430093 + SAMN39900234 + GSM8072839 + + OA2-1_Condition_NWB_Rep2 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430093 + SAMN39900234 + GSM8072839 + + + + + + + SRR27928102 + GSM8072839_r1 + + + + GSM8072839_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430093 + SAMN39900234 + GSM8072839 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585131 + GSM8072838_r1 + + GSM8072838: OA1-2_Condition_WB_Rep1; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430094 + GSM8072838 + + + + GSM8072838 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430094 + SAMN39900235 + GSM8072838 + + OA1-2_Condition_WB_Rep1 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430094 + SAMN39900235 + GSM8072838 + + + + + + + SRR27928103 + GSM8072838_r1 + + + + GSM8072838_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430094 + SAMN39900235 + GSM8072838 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585130 + GSM8072837_r1 + + GSM8072837: OA1-1_Condition_NWB_Rep1; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430092 + GSM8072837 + + + + GSM8072837 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430092 + SAMN39900236 + GSM8072837 + + OA1-1_Condition_NWB_Rep1 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430092 + SAMN39900236 + GSM8072837 + + + + + + + SRR27928104 + GSM8072837_r1 + + + + GSM8072837_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430092 + SAMN39900236 + GSM8072837 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585129 + GSM8072836_r1 + + GSM8072836: C3_Condition_Control_Rep3; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430095 + GSM8072836 + + + + GSM8072836 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430095 + SAMN39900237 + GSM8072836 + + C3_Condition_Control_Rep3 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430095 + SAMN39900237 + GSM8072836 + + + + + + + SRR27928105 + GSM8072836_r1 + + + + GSM8072836_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430095 + SAMN39900237 + GSM8072836 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585128 + GSM8072835_r1 + + GSM8072835: C2_Condition_Control_Rep2; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430091 + GSM8072835 + + + + GSM8072835 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430091 + SAMN39900238 + GSM8072835 + + C2_Condition_Control_Rep2 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430091 + SAMN39900238 + GSM8072835 + + + + + + + SRR27928106 + GSM8072835_r1 + + + + GSM8072835_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430091 + SAMN39900238 + GSM8072835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23585127 + GSM8072834_r1 + + GSM8072834: C1_Condition_Control_Rep1; Homo sapiens; RNA-Seq + + + SRP489126 + PRJNA1075064 + + + + + + + SRS20430090 + GSM8072834 + + + + GSM8072834 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1800512 + SUB14216157 + + + + Xi'an Jiaotong University + +
+ xiwulu157# + Xi'an + State + China +
+ + yang + wei + + + + + + SRP489126 + PRJNA1075064 + GSE255460 + + + Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls + + Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations. Overall design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors + GSE255460 + + + + + pubmed + 38325908 + + + + + + + SRS20430090 + SAMN39900239 + GSM8072834 + + C1_Condition_Control_Rep1 + + 9606 + Homo sapiens + + + + + bioproject + 1075064 + + + + + + + source_name + Cartilage + + + tissue + Cartilage + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20430090 + SAMN39900239 + GSM8072834 + + + + + + + SRR27928107 + GSM8072834_r1 + + + + GSM8072834_r1 + + + + + loader + fastq-load.py + + + + + + SRS20430090 + SAMN39900239 + GSM8072834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE261494.xml b/tests/data/GSE261494.xml new file mode 100644 index 0000000..73351e8 --- /dev/null +++ b/tests/data/GSE261494.xml @@ -0,0 +1,4744 @@ + + + + + + + SRX23939332 + GSM8145360_r1 + + GSM8145360: 12_female PDMCAO aged #2; Mus musculus; RNA-Seq + + + SRP495009 + PRJNA1087307 + + + + + + + SRS20743013 + GSM8145360 + + + + GSM8145360 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + brains slice, Miltenyi Adult Brain Dissociation Kitt 10X Genomics + + + + + NextSeq 500 + + + + + + SRA1823508 + SUB14310122 + + + + Department of Neurology, The University of Texas Health Science Center at Houston + +
+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743013 + SAMN40439333 + GSM8145360 + + 12_female PDMCAO aged #2 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + aged + + + genotype + female + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743013 + SAMN40439333 + GSM8145360 + + + + + + + SRR28331002 + GSM8145360_r1 + + + + GSM8145360_r1 + + + + + + SRS20743013 + SAMN40439333 + GSM8145360 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743011 + SAMN40439335 + GSM8145358 + + 10_female PDMCAO young #2 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + young + + + genotype + female + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743011 + SAMN40439335 + GSM8145358 + + + + + + + SRR28331010 + GSM8145358_r1 + + + + GSM8145358_r1 + + + + + + SRS20743011 + SAMN40439335 + GSM8145358 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743010 + SAMN40439336 + GSM8145357 + + 9_male PDMCAO young #2 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + young + + + genotype + male + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743010 + SAMN40439336 + GSM8145357 + + + + + + + SRR28331014 + GSM8145357_r1 + + + + GSM8145357_r1 + + + + + + SRS20743010 + SAMN40439336 + GSM8145357 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743009 + SAMN40439337 + GSM8145356 + + 8_female PDMCAO aged #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + aged + + + genotype + female + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743009 + SAMN40439337 + GSM8145356 + + + + + + + SRR28331018 + GSM8145356_r1 + + + + GSM8145356_r1 + + + + + + SRS20743009 + SAMN40439337 + GSM8145356 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743008 + SAMN40439338 + GSM8145355 + + 7_male PDMCAO aged #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + aged + + + genotype + male + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743008 + SAMN40439338 + GSM8145355 + + + + + + + SRR28331022 + GSM8145355_r1 + + + + GSM8145355_r1 + + + + + + SRS20743008 + SAMN40439338 + GSM8145355 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743007 + SAMN40439339 + GSM8145354 + + 6_female PDMCAO young #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + young + + + genotype + female + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743007 + SAMN40439339 + GSM8145354 + + + + + + + SRR28331026 + GSM8145354_r1 + + + + GSM8145354_r1 + + + + + + SRS20743007 + SAMN40439339 + GSM8145354 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743006 + SAMN40439340 + GSM8145353 + + 5_male PDMCAO young #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + young + + + genotype + male + + + treatment + PDMCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743006 + SAMN40439340 + GSM8145353 + + + + + + + SRR28331030 + GSM8145353_r1 + + + + GSM8145353_r1 + + + + + + SRS20743006 + SAMN40439340 + GSM8145353 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23939324 + GSM8145352_r1 + + GSM8145352: 4_female sham aged #1; Mus musculus; RNA-Seq + + + SRP495009 + PRJNA1087307 + + + + + + + SRS20743005 + GSM8145352 + + + + GSM8145352 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + brains slice, Miltenyi Adult Brain Dissociation Kitt 10X Genomics + + + + + NextSeq 500 + + + + + + SRA1823508 + SUB14310122 + + + + Department of Neurology, The University of Texas Health Science Center at Houston + +
+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743005 + SAMN40439341 + GSM8145352 + + 4_female sham aged #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + aged + + + genotype + female + + + treatment + sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743005 + SAMN40439341 + GSM8145352 + + + + + + + SRR28331034 + GSM8145352_r1 + + + + GSM8145352_r1 + + + + + + SRS20743005 + SAMN40439341 + GSM8145352 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23939323 + GSM8145351_r1 + + GSM8145351: 3_male sham aged #1; Mus musculus; RNA-Seq + + + SRP495009 + PRJNA1087307 + + + + + + + SRS20743004 + GSM8145351 + + + + GSM8145351 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + brains slice, Miltenyi Adult Brain Dissociation Kitt 10X Genomics + + + + + NextSeq 500 + + + + + + SRA1823508 + SUB14310122 + + + + Department of Neurology, The University of Texas Health Science Center at Houston + +
+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743004 + SAMN40439342 + GSM8145351 + + 3_male sham aged #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + aged + + + genotype + male + + + treatment + sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743004 + SAMN40439342 + GSM8145351 + + + + + + + SRR28331038 + GSM8145351_r1 + + + + GSM8145351_r1 + + + + + + SRS20743004 + SAMN40439342 + GSM8145351 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX23939322 + GSM8145350_r1 + + GSM8145350: 2_female sham young #1; Mus musculus; RNA-Seq + + + SRP495009 + PRJNA1087307 + + + + + + + SRS20743003 + GSM8145350 + + + + GSM8145350 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + brains slice, Miltenyi Adult Brain Dissociation Kitt 10X Genomics + + + + + NextSeq 500 + + + + + + SRA1823508 + SUB14310122 + + + + Department of Neurology, The University of Texas Health Science Center at Houston + +
+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743003 + SAMN40439343 + GSM8145350 + + 2_female sham young #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Young + + + genotype + female + + + treatment + sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743003 + SAMN40439343 + GSM8145350 + + + + + + + SRR28331042 + GSM8145350_r1 + + + + GSM8145350_r1 + + + + + + SRS20743003 + SAMN40439343 + GSM8145350 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR28331044 + GSM8145350_r3 + + + + GSM8145350_r1 + + + + + + SRS20743003 + SAMN40439343 + GSM8145350 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28331045 + GSM8145350_r4 + + + + GSM8145350_r1 + + + + + + SRS20743003 + SAMN40439343 + GSM8145350 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23939321 + GSM8145349_r1 + + GSM8145349: 1_male sham young #1; Mus musculus; RNA-Seq + + + SRP495009 + PRJNA1087307 + + + + + + + SRS20743002 + GSM8145349 + + + + GSM8145349 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + brains slice, Miltenyi Adult Brain Dissociation Kitt 10X Genomics + + + + + NextSeq 500 + + + + + + SRA1823508 + SUB14310122 + + + + Department of Neurology, The University of Texas Health Science Center at Houston + +
+ 6431 Fannin St. + Houston, + TX + USA +
+ + Gab Seok + Kim + + + + + + SRP495009 + PRJNA1087307 + GSE261494 + + + Ifi27l2a regulates the microglial inflammation in the context of aging and stroke + + Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia. Overall design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq. + GSE261494 + + + + + pubmed + 39953063 + + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + 1_male sham young #1 + + 10090 + Mus musculus + + + + + bioproject + 1087307 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Young + + + genotype + male + + + treatment + sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + + + + + + SRR28331046 + GSM8145349_r1 + + + + GSM8145349_r1 + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28331047 + GSM8145349_r2 + + + + GSM8145349_r1 + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28331048 + GSM8145349_r3 + + + + GSM8145349_r1 + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28331049 + GSM8145349_r4 + + + + GSM8145349_r1 + + + + + + SRS20743002 + SAMN40439344 + GSM8145349 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE261596.xml b/tests/data/GSE261596.xml new file mode 100644 index 0000000..639bfc9 --- /dev/null +++ b/tests/data/GSE261596.xml @@ -0,0 +1,2608 @@ + + + + + + + SRX23952937 + GSM8147278_r1 + + GSM8147278: S12, Hippocampus, wild-type, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753432 + GSM8147278 + + + + GSM8147278 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753432 + SAMN40460212 + GSM8147278 + + S12, Hippocampus, wild-type, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753432 + SAMN40460212 + GSM8147278 + + + + + + + SRR28346414 + GSM8147278_r1 + + + + GSM8147278_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753432 + SAMN40460212 + GSM8147278 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952936 + GSM8147277_r1 + + GSM8147277: S11, Hippocampus, wild-type, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753431 + GSM8147277 + + + + GSM8147277 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753431 + SAMN40460213 + GSM8147277 + + S11, Hippocampus, wild-type, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753431 + SAMN40460213 + GSM8147277 + + + + + + + SRR28346415 + GSM8147277_r1 + + + + GSM8147277_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753431 + SAMN40460213 + GSM8147277 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952935 + GSM8147275_r1 + + GSM8147275: S10, Hippocampus, 3xTg-AD, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753430 + GSM8147275 + + + + GSM8147275 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753430 + SAMN40460214 + GSM8147275 + + S10, Hippocampus, 3xTg-AD, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753430 + SAMN40460214 + GSM8147275 + + + + + + + SRR28346416 + GSM8147275_r1 + + + + GSM8147275_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753430 + SAMN40460214 + GSM8147275 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952934 + GSM8147274_r1 + + GSM8147274: S9, Hippocampus, 3xTg-AD, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753429 + GSM8147274 + + + + GSM8147274 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753429 + SAMN40460215 + GSM8147274 + + S9, Hippocampus, 3xTg-AD, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753429 + SAMN40460215 + GSM8147274 + + + + + + + SRR28346417 + GSM8147274_r1 + + + + GSM8147274_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753429 + SAMN40460215 + GSM8147274 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952933 + GSM8147273_r1 + + GSM8147273: S8, Hippocampus, wild-type, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753428 + GSM8147273 + + + + GSM8147273 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753428 + SAMN40460216 + GSM8147273 + + S8, Hippocampus, wild-type, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753428 + SAMN40460216 + GSM8147273 + + + + + + + SRR28346418 + GSM8147273_r1 + + + + GSM8147273_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753428 + SAMN40460216 + GSM8147273 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952932 + GSM8147272_r1 + + GSM8147272: S7, Hippocampus, wild-type, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753426 + GSM8147272 + + + + GSM8147272 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753426 + SAMN40460217 + GSM8147272 + + S7, Hippocampus, wild-type, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753426 + SAMN40460217 + GSM8147272 + + + + + + + SRR28346419 + GSM8147272_r1 + + + + GSM8147272_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753426 + SAMN40460217 + GSM8147272 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952931 + GSM8147271_r1 + + GSM8147271: S6, Hippocampus, 3xTg-AD, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753427 + GSM8147271 + + + + GSM8147271 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753427 + SAMN40460218 + GSM8147271 + + S6, Hippocampus, 3xTg-AD, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753427 + SAMN40460218 + GSM8147271 + + + + + + + SRR28346420 + GSM8147271_r1 + + + + GSM8147271_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753427 + SAMN40460218 + GSM8147271 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952930 + GSM8147270_r1 + + GSM8147270: S5, Hippocampus, 3xTg-AD, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753425 + GSM8147270 + + + + GSM8147270 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753425 + SAMN40460219 + GSM8147270 + + S5, Hippocampus, 3xTg-AD, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753425 + SAMN40460219 + GSM8147270 + + + + + + + SRR28346421 + GSM8147270_r1 + + + + GSM8147270_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753425 + SAMN40460219 + GSM8147270 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952929 + GSM8147269_r1 + + GSM8147269: S4, Hippocampus, wild-type, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753424 + GSM8147269 + + + + GSM8147269 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753424 + SAMN40460220 + GSM8147269 + + S4, Hippocampus, wild-type, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753424 + SAMN40460220 + GSM8147269 + + + + + + + SRR28346422 + GSM8147269_r1 + + + + GSM8147269_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753424 + SAMN40460220 + GSM8147269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952928 + GSM8147268_r1 + + GSM8147268: S3, Hippocampus, wild-type, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753423 + GSM8147268 + + + + GSM8147268 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753423 + SAMN40460221 + GSM8147268 + + S3, Hippocampus, wild-type, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + wild-type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753423 + SAMN40460221 + GSM8147268 + + + + + + + SRR28346423 + GSM8147268_r1 + + + + GSM8147268_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753423 + SAMN40460221 + GSM8147268 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952927 + GSM8147267_r1 + + GSM8147267: S2, Hippocampus, 3xTg-AD, 12m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753422 + GSM8147267 + + + + GSM8147267 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753422 + SAMN40460222 + GSM8147267 + + S2, Hippocampus, 3xTg-AD, 12m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 12 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753422 + SAMN40460222 + GSM8147267 + + + + + + + SRR28346424 + GSM8147267_r1 + + + + GSM8147267_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753422 + SAMN40460222 + GSM8147267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX23952926 + GSM8147266_r1 + + GSM8147266: S1, Hippocampus, 3xTg-AD, 6m; Mus musculus; RNA-Seq + + + SRP495269 + PRJNA1088080 + + + + + + + SRS20753421 + GSM8147266 + + + + GSM8147266 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + We adapted our single nuclei isolation for mouse hippocampus samples from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II. Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition hippocampal nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1824466 + SUB14313749 + + + + Cell, Developmental and Integrative Biology, University of Alabama at Birmingham + +
+ 1900 University Blvd + Birmingham + USA +
+ + Bradley + Yoder + + + + + + SRP495269 + PRJNA1088080 + GSE261596 + + + Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points + + Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-ß plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss. Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-ß and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses. Overall design: We anesthetized and perfused 3xTg-AD mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax: JAX MMRRC Stock# 034830) and wild-type littermates before dissecting brain regions to obtain hippocampal samples. We isolated nuclei from the left hippocampus of 12 female mice (6 3xTg-AD, 6 wild-type) from two time points (6 and 12 months; n = 6 per time point). The 3xTg-AD mouse model exhibits amyloid-ß and tau pathology occurring as early as 6 and 12 months, respectively. + GSE261596 + + + + + pubmed + 40026671 + + + + + pubmed + 38826305 + + + + + + + SRS20753421 + SAMN40460223 + GSM8147266 + + S1, Hippocampus, 3xTg-AD, 6m + + 10090 + Mus musculus + + + + + bioproject + 1088080 + + + + + + + source_name + left hippocampus + + + tissue + left hippocampus + + + age + 6 months + + + Sex + female + + + genotype + 3xTg-AD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20753421 + SAMN40460223 + GSM8147266 + + + + + + + SRR28346425 + GSM8147266_r1 + + + + GSM8147266_r1 + + + + + loader + fastq-load.py + + + + + + SRS20753421 + SAMN40460223 + GSM8147266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE263191.xml b/tests/data/GSE263191.xml new file mode 100644 index 0000000..99b75d1 --- /dev/null +++ b/tests/data/GSE263191.xml @@ -0,0 +1,3220 @@ + + + + + + + SRX24151722 + GSM8187377_r1 + + GSM8187377: PFC, BCAS, Female, 4; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933184 + GSM8187377 + + + + GSM8187377 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + PFC, BCAS, Female, 4 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + BCAS + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + + + + + + SRR28552118 + GSM8187377_r1 + + + + GSM8187377_r1 + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552119 + GSM8187377_r2 + + + + GSM8187377_r1 + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552120 + GSM8187377_r3 + + + + GSM8187377_r1 + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552121 + GSM8187377_r4 + + + + GSM8187377_r1 + + + + + + SRS20933184 + SAMN40744938 + GSM8187377 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151721 + GSM8187376_r1 + + GSM8187376: PFC, BCAS, Female, 3; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933183 + GSM8187376 + + + + GSM8187376 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + PFC, BCAS, Female, 3 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + BCAS + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + + + + + + SRR28552122 + GSM8187376_r1 + + + + GSM8187376_r1 + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552123 + GSM8187376_r2 + + + + GSM8187376_r1 + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552124 + GSM8187376_r3 + + + + GSM8187376_r1 + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552125 + GSM8187376_r4 + + + + GSM8187376_r1 + + + + + + SRS20933183 + SAMN40744939 + GSM8187376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151720 + GSM8187375_r1 + + GSM8187375: PFC, BCAS, Male, 2; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933182 + GSM8187375 + + + + GSM8187375 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + PFC, BCAS, Male, 2 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + BCAS + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + + + + + + SRR28552126 + GSM8187375_r1 + + + + GSM8187375_r1 + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552127 + GSM8187375_r2 + + + + GSM8187375_r1 + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552128 + GSM8187375_r3 + + + + GSM8187375_r1 + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552129 + GSM8187375_r4 + + + + GSM8187375_r1 + + + + + + SRS20933182 + SAMN40744940 + GSM8187375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151719 + GSM8187374_r1 + + GSM8187374: PFC, BCAS, Male, 1; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933181 + GSM8187374 + + + + GSM8187374 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + PFC, BCAS, Male, 1 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + BCAS + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + + + + + + SRR28552130 + GSM8187374_r1 + + + + GSM8187374_r1 + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552131 + GSM8187374_r2 + + + + GSM8187374_r1 + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552132 + GSM8187374_r3 + + + + GSM8187374_r1 + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552133 + GSM8187374_r4 + + + + GSM8187374_r1 + + + + + + SRS20933181 + SAMN40744941 + GSM8187374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151718 + GSM8187373_r1 + + GSM8187373: PFC, Sham, Female, 4; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933180 + GSM8187373 + + + + GSM8187373 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + PFC, Sham, Female, 4 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + Sham + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + + + + + + SRR28552134 + GSM8187373_r1 + + + + GSM8187373_r1 + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552135 + GSM8187373_r2 + + + + GSM8187373_r1 + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552136 + GSM8187373_r3 + + + + GSM8187373_r1 + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552137 + GSM8187373_r4 + + + + GSM8187373_r1 + + + + + + SRS20933180 + SAMN40744942 + GSM8187373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151717 + GSM8187372_r1 + + GSM8187372: PFC, Sham, Female, 3; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933179 + GSM8187372 + + + + GSM8187372 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + PFC, Sham, Female, 3 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + Sham + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + + + + + + SRR28552138 + GSM8187372_r1 + + + + GSM8187372_r1 + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552139 + GSM8187372_r2 + + + + GSM8187372_r1 + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552140 + GSM8187372_r3 + + + + GSM8187372_r1 + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552141 + GSM8187372_r4 + + + + GSM8187372_r1 + + + + + + SRS20933179 + SAMN40744943 + GSM8187372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151716 + GSM8187371_r1 + + GSM8187371: PFC, Sham, Male, 2; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933178 + GSM8187371 + + + + GSM8187371 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + PFC, Sham, Male, 2 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + Sham + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + + + + + + SRR28552142 + GSM8187371_r1 + + + + GSM8187371_r1 + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552143 + GSM8187371_r2 + + + + GSM8187371_r1 + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552144 + GSM8187371_r3 + + + + GSM8187371_r1 + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552145 + GSM8187371_r4 + + + + GSM8187371_r1 + + + + + + SRS20933178 + SAMN40744944 + GSM8187371 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24151715 + GSM8187370_r1 + + GSM8187370: PFC, Sham, Male, 1; Mus musculus; RNA-Seq + + + SRP499663 + PRJNA1096111 + + + + + + + SRS20933177 + GSM8187370 + + + + GSM8187370 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer. 10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1839466 + SUB14357955 + + + + Nanyang Technological University + +
+ 50 Nanyang Ave + Singapore + Singapore +
+ + Meng How + Tan + + + + + + SRP499663 + PRJNA1096111 + GSE263191 + + + Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation + + Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion. Overall design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed. + GSE263191 + + + + + pubmed + 40628749 + + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + PFC, Sham, Male, 1 + + 10090 + Mus musculus + + + + + bioproject + 1096111 + + + + + + + source_name + Prefrontal cortex + + + age + 80 days + + + tissue + Prefrontal cortex + + + cell type + Mixed + + + genotype + C57BL/6J + + + treatment + Sham + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + + + + + + SRR28552146 + GSM8187370_r1 + + + + GSM8187370_r1 + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552147 + GSM8187370_r2 + + + + GSM8187370_r1 + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552148 + GSM8187370_r3 + + + + GSM8187370_r1 + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28552149 + GSM8187370_r4 + + + + GSM8187370_r1 + + + + + + SRS20933177 + SAMN40744945 + GSM8187370 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE263392.xml b/tests/data/GSE263392.xml new file mode 100644 index 0000000..154b850 --- /dev/null +++ b/tests/data/GSE263392.xml @@ -0,0 +1,5536 @@ + + + + + + + SRX24186135 + GSM8190807_r1 + + GSM8190807: ret/wt, biol rep 6, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960580 + GSM8190807 + + + + GSM8190807 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960580 + SAMN40870224 + GSM8190807 + + ret/wt, biol rep 6, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 7d + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960580 + SAMN40870224 + GSM8190807 + + + + + + + SRR28586633 + GSM8190807_r1 + + + + GSM8190807_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960580 + SAMN40870224 + GSM8190807 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28586634 + GSM8190807_r2 + + + + GSM8190807_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960580 + SAMN40870224 + GSM8190807 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186134 + GSM8190806_r1 + + GSM8190806: ret/wt, biol rep 6, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960582 + GSM8190806 + + + + GSM8190806 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960582 + SAMN40870225 + GSM8190806 + + ret/wt, biol rep 6, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 7d + + + Sex + male + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960582 + SAMN40870225 + GSM8190806 + + + + + + + SRR28586635 + GSM8190806_r1 + + + + GSM8190806_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960582 + SAMN40870225 + GSM8190806 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28586636 + GSM8190806_r2 + + + + GSM8190806_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960582 + SAMN40870225 + GSM8190806 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186133 + GSM8190805_r1 + + GSM8190805: ret/ret, biol rep 6, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960579 + GSM8190805 + + + + GSM8190805 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960579 + SAMN40870226 + GSM8190805 + + ret/ret, biol rep 6, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 9d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960579 + SAMN40870226 + GSM8190805 + + + + + + + SRR28586637 + GSM8190805_r1 + + + + GSM8190805_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960579 + SAMN40870226 + GSM8190805 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28586638 + GSM8190805_r2 + + + + GSM8190805_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960579 + SAMN40870226 + GSM8190805 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186132 + GSM8190804_r1 + + GSM8190804: ret/ret, biol rep 6, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960577 + GSM8190804 + + + + GSM8190804 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960577 + SAMN40870227 + GSM8190804 + + ret/ret, biol rep 6, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 9d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960577 + SAMN40870227 + GSM8190804 + + + + + + + SRR28586639 + GSM8190804_r1 + + + + GSM8190804_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960577 + SAMN40870227 + GSM8190804 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28586640 + GSM8190804_r2 + + + + GSM8190804_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960577 + SAMN40870227 + GSM8190804 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186131 + GSM8190803_r1 + + GSM8190803: ret/wt, biol rep 5, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960578 + GSM8190803 + + + + GSM8190803 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960578 + SAMN40870228 + GSM8190803 + + ret/wt, biol rep 5, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 9d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960578 + SAMN40870228 + GSM8190803 + + + + + + + SRR28586641 + GSM8190803_r1 + + + + GSM8190803_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960578 + SAMN40870228 + GSM8190803 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186130 + GSM8190802_r1 + + GSM8190802: ret/wt, biol rep 5, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960576 + GSM8190802 + + + + GSM8190802 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960576 + SAMN40870229 + GSM8190802 + + ret/wt, biol rep 5, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 9d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960576 + SAMN40870229 + GSM8190802 + + + + + + + SRR28586642 + GSM8190802_r1 + + + + GSM8190802_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960576 + SAMN40870229 + GSM8190802 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186129 + GSM8190801_r1 + + GSM8190801: ret/ret, biol rep 5, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960575 + GSM8190801 + + + + GSM8190801 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960575 + SAMN40870230 + GSM8190801 + + ret/ret, biol rep 5, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 7d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960575 + SAMN40870230 + GSM8190801 + + + + + + + SRR28586643 + GSM8190801_r1 + + + + GSM8190801_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960575 + SAMN40870230 + GSM8190801 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186128 + GSM8190800_r1 + + GSM8190800: ret/ret, biol rep 5, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960571 + GSM8190800 + + + + GSM8190800 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960571 + SAMN40870231 + GSM8190800 + + ret/ret, biol rep 5, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 7d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960571 + SAMN40870231 + GSM8190800 + + + + + + + SRR28586644 + GSM8190800_r1 + + + + GSM8190800_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960571 + SAMN40870231 + GSM8190800 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186127 + GSM8190799_r1 + + GSM8190799: ret/ret, biol rep 4, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960574 + GSM8190799 + + + + GSM8190799 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960574 + SAMN40870232 + GSM8190799 + + ret/ret, biol rep 4, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 24d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960574 + SAMN40870232 + GSM8190799 + + + + + + + SRR28586645 + GSM8190799_r1 + + + + GSM8190799_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960574 + SAMN40870232 + GSM8190799 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186126 + GSM8190798_r1 + + GSM8190798: ret/ret, biol rep 4, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960573 + GSM8190798 + + + + GSM8190798 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960573 + SAMN40870233 + GSM8190798 + + ret/ret, biol rep 4, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 4m 24d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960573 + SAMN40870233 + GSM8190798 + + + + + + + SRR28586646 + GSM8190798_r1 + + + + GSM8190798_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960573 + SAMN40870233 + GSM8190798 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186125 + GSM8190797_r1 + + GSM8190797: ret/wt, biol rep 4, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960572 + GSM8190797 + + + + GSM8190797 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960572 + SAMN40870234 + GSM8190797 + + ret/wt, biol rep 4, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 24d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960572 + SAMN40870234 + GSM8190797 + + + + + + + SRR28586647 + GSM8190797_r1 + + + + GSM8190797_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960572 + SAMN40870234 + GSM8190797 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186124 + GSM8190796_r1 + + GSM8190796: ret/wt, biol rep 4, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960570 + GSM8190796 + + + + GSM8190796 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960570 + SAMN40870235 + GSM8190796 + + ret/wt, biol rep 4, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 4m 24d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960570 + SAMN40870235 + GSM8190796 + + + + + + + SRR28586648 + GSM8190796_r1 + + + + GSM8190796_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960570 + SAMN40870235 + GSM8190796 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186123 + GSM8190795_r1 + + GSM8190795: ret/ret, biol rep 3, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960569 + GSM8190795 + + + + GSM8190795 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960569 + SAMN40870236 + GSM8190795 + + ret/ret, biol rep 3, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m 18d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960569 + SAMN40870236 + GSM8190795 + + + + + + + SRR28586649 + GSM8190795_r1 + + + + GSM8190795_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960569 + SAMN40870236 + GSM8190795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186122 + GSM8190794_r1 + + GSM8190794: ret/ret, biol rep 3, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960568 + GSM8190794 + + + + GSM8190794 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960568 + SAMN40870237 + GSM8190794 + + ret/ret, biol rep 3, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m 18d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960568 + SAMN40870237 + GSM8190794 + + + + + + + SRR28586650 + GSM8190794_r1 + + + + GSM8190794_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960568 + SAMN40870237 + GSM8190794 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186121 + GSM8190793_r1 + + GSM8190793: ret/wt, biol rep 3, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960567 + GSM8190793 + + + + GSM8190793 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960567 + SAMN40870238 + GSM8190793 + + ret/wt, biol rep 3, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m 18d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960567 + SAMN40870238 + GSM8190793 + + + + + + + SRR28586651 + GSM8190793_r1 + + + + GSM8190793_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960567 + SAMN40870238 + GSM8190793 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186120 + GSM8190792_r1 + + GSM8190792: ret/wt, biol rep 3, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960566 + GSM8190792 + + + + GSM8190792 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960566 + SAMN40870239 + GSM8190792 + + ret/wt, biol rep 3, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m 18d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960566 + SAMN40870239 + GSM8190792 + + + + + + + SRR28586652 + GSM8190792_r1 + + + + GSM8190792_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960566 + SAMN40870239 + GSM8190792 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186119 + GSM8190791_r1 + + GSM8190791: ret/ret, biol rep 2, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960565 + GSM8190791 + + + + GSM8190791 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960565 + SAMN40870240 + GSM8190791 + + ret/ret, biol rep 2, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960565 + SAMN40870240 + GSM8190791 + + + + + + + SRR28586653 + GSM8190791_r1 + + + + GSM8190791_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960565 + SAMN40870240 + GSM8190791 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186118 + GSM8190790_r1 + + GSM8190790: ret/ret, biol rep 2, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960562 + GSM8190790 + + + + GSM8190790 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960562 + SAMN40870241 + GSM8190790 + + ret/ret, biol rep 2, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960562 + SAMN40870241 + GSM8190790 + + + + + + + SRR28586654 + GSM8190790_r1 + + + + GSM8190790_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960562 + SAMN40870241 + GSM8190790 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186117 + GSM8190789_r1 + + GSM8190789: ret/wt, biol rep 2, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960564 + GSM8190789 + + + + GSM8190789 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960564 + SAMN40870242 + GSM8190789 + + ret/wt, biol rep 2, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960564 + SAMN40870242 + GSM8190789 + + + + + + + SRR28586655 + GSM8190789_r1 + + + + GSM8190789_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960564 + SAMN40870242 + GSM8190789 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186116 + GSM8190788_r1 + + GSM8190788: ret/wt, biol rep 2, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960560 + GSM8190788 + + + + GSM8190788 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960560 + SAMN40870243 + GSM8190788 + + ret/wt, biol rep 2, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960560 + SAMN40870243 + GSM8190788 + + + + + + + SRR28586656 + GSM8190788_r1 + + + + GSM8190788_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960560 + SAMN40870243 + GSM8190788 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186115 + GSM8190787_r1 + + GSM8190787: ret/wt, biol rep 1, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960563 + GSM8190787 + + + + GSM8190787 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960563 + SAMN40870244 + GSM8190787 + + ret/wt, biol rep 1, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m 3d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960563 + SAMN40870244 + GSM8190787 + + + + + + + SRR28586657 + GSM8190787_r1 + + + + GSM8190787_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960563 + SAMN40870244 + GSM8190787 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186114 + GSM8190786_r1 + + GSM8190786: ret/wt, biol rep 1, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960561 + GSM8190786 + + + + GSM8190786 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960561 + SAMN40870245 + GSM8190786 + + ret/wt, biol rep 1, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/wt + + + age + 5m 3d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960561 + SAMN40870245 + GSM8190786 + + + + + + + SRR28586658 + GSM8190786_r1 + + + + GSM8190786_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960561 + SAMN40870245 + GSM8190786 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186113 + GSM8190785_r1 + + GSM8190785: ret/ret, biol rep 1, ctx; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960559 + GSM8190785 + + + + GSM8190785 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960559 + SAMN40870246 + GSM8190785 + + ret/ret, biol rep 1, ctx + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: cortical regions + + + tissue + brain: cortical regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m 3d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960559 + SAMN40870246 + GSM8190785 + + + + + + + SRR28586659 + GSM8190785_r1 + + + + GSM8190785_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960559 + SAMN40870246 + GSM8190785 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24186112 + GSM8190784_r1 + + GSM8190784: ret/ret, biol rep 1, db; Mus musculus; RNA-Seq + + + SRP500252 + PRJNA1097378 + + + + + + + SRS20960558 + GSM8190784 + + + + GSM8190784 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Tissue was processed for single nuclei isolation as previously described in Zhou et al. (Zhou et al., 2020). Isolated mouse nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5′ Reagent Kits per the manufacturer's instructions (10x Genomics). Library type = 10x 5'GEX V2, Dual Index + + + + + Illumina NovaSeq 6000 + + + + + + SRA1841952 + SUB14366250 + + + + Swiss Institute of Bioinformatics + +
+ Rue du Bugnon 25A + Lausanne + Switzerland +
+ + Tania + Wyss + + + + + + SRP500252 + PRJNA1097378 + GSE263392 + + + Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice + + Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications: Overall design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions. + GSE263392 + + + + + pubmed + 39467636 + + + + + + + SRS20960558 + SAMN40870247 + GSM8190784 + + ret/ret, biol rep 1, db + + 10090 + Mus musculus + + + + + bioproject + 1097378 + + + + + + + source_name + brain: deep brain regions + + + tissue + brain: deep brain regions + + + cell type + nuclei + + + strain + B6.Pdgfbtm3Cbet + + + genotype + Pdgfbret/ret + + + age + 5m 3d + + + Sex + female + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS20960558 + SAMN40870247 + GSM8190784 + + + + + + + SRR28586660 + GSM8190784_r1 + + + + GSM8190784_r1 + + + + + loader + fastq-load.py + + + + + + SRS20960558 + SAMN40870247 + GSM8190784 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE264408.xml b/tests/data/GSE264408.xml new file mode 100644 index 0000000..a4b5017 --- /dev/null +++ b/tests/data/GSE264408.xml @@ -0,0 +1,2164 @@ + + + + + + + SRX24312649 + GSM8217734_r1 + + GSM8217734: Mouse colon, ChronicColitis4; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074419 + GSM8217734 + + + + GSM8217734 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074419 + SAMN41019954 + GSM8217734 + + Mouse colon, ChronicColitis4 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Chronic Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074419 + SAMN41019954 + GSM8217734 + + + + + + + SRR28746893 + GSM8217734_r1 + + + + GSM8217734_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074419 + SAMN41019954 + GSM8217734 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312648 + GSM8217733_r1 + + GSM8217733: Mouse colon, ChronicColitis3; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074418 + GSM8217733 + + + + GSM8217733 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074418 + SAMN41019955 + GSM8217733 + + Mouse colon, ChronicColitis3 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Chronic Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074418 + SAMN41019955 + GSM8217733 + + + + + + + SRR28746891 + GSM8217733_r1 + + + + GSM8217733_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074418 + SAMN41019955 + GSM8217733 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312647 + GSM8217732_r1 + + GSM8217732: Mouse colon, ChronicColitis2; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074417 + GSM8217732 + + + + GSM8217732 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074417 + SAMN41019956 + GSM8217732 + + Mouse colon, ChronicColitis2 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Chronic Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074417 + SAMN41019956 + GSM8217732 + + + + + + + SRR28746892 + GSM8217732_r1 + + + + GSM8217732_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074417 + SAMN41019956 + GSM8217732 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312646 + GSM8217731_r1 + + GSM8217731: Mouse colon, ChronicColitis1; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074416 + GSM8217731 + + + + GSM8217731 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074416 + SAMN41019957 + GSM8217731 + + Mouse colon, ChronicColitis1 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Chronic Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074416 + SAMN41019957 + GSM8217731 + + + + + + + SRR28746894 + GSM8217731_r1 + + + + GSM8217731_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074416 + SAMN41019957 + GSM8217731 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312645 + GSM8217730_r1 + + GSM8217730: Mouse colon, AcuteColitis3; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074415 + GSM8217730 + + + + GSM8217730 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074415 + SAMN41019958 + GSM8217730 + + Mouse colon, AcuteColitis3 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Acute Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074415 + SAMN41019958 + GSM8217730 + + + + + + + SRR28746895 + GSM8217730_r1 + + + + GSM8217730_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074415 + SAMN41019958 + GSM8217730 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312644 + GSM8217729_r1 + + GSM8217729: Mouse colon, AcuteColitis2; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074413 + GSM8217729 + + + + GSM8217729 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074413 + SAMN41019959 + GSM8217729 + + Mouse colon, AcuteColitis2 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Acute Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074413 + SAMN41019959 + GSM8217729 + + + + + + + SRR28746898 + GSM8217729_r1 + + + + GSM8217729_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074413 + SAMN41019959 + GSM8217729 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312643 + GSM8217728_r1 + + GSM8217728: Mouse colon, AcuteColitis1; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074414 + GSM8217728 + + + + GSM8217728 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074414 + SAMN41019960 + GSM8217728 + + Mouse colon, AcuteColitis1 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Acute Colitis + + + treatment + dextran sodium sulfate dissolved in drinking water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074414 + SAMN41019960 + GSM8217728 + + + + + + + SRR28746896 + GSM8217728_r1 + + + + GSM8217728_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074414 + SAMN41019960 + GSM8217728 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312642 + GSM8217727_r1 + + GSM8217727: Mouse colon, Healthy3; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074412 + GSM8217727 + + + + GSM8217727 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074412 + SAMN41019961 + GSM8217727 + + Mouse colon, Healthy3 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Healthy + + + treatment + sterile distilled water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074412 + SAMN41019961 + GSM8217727 + + + + + + + SRR28746897 + GSM8217727_r1 + + + + GSM8217727_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074412 + SAMN41019961 + GSM8217727 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312641 + GSM8217726_r1 + + GSM8217726: Mouse colon, Healthy2; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074411 + GSM8217726 + + + + GSM8217726 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074411 + SAMN41019962 + GSM8217726 + + Mouse colon, Healthy2 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Healthy + + + treatment + sterile distilled water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074411 + SAMN41019962 + GSM8217726 + + + + + + + SRR28746899 + GSM8217726_r1 + + + + GSM8217726_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074411 + SAMN41019962 + GSM8217726 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24312640 + GSM8217725_r1 + + GSM8217725: Mouse colon, Healthy1; Mus musculus; RNA-Seq + + + SRP502899 + PRJNA1102362 + + + + + + + SRS21074410 + GSM8217725 + + + + GSM8217725 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis. We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea). + + + + + HiSeq X Ten + + + + + + SRA1849610 + SUB14390830 + + + + Machine Learning & Bioinformatics Lab, Electronics and Electrical Eng., Dankook University + +
+ Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu + Yongin-si + Gyeonggi-do + South Korea +
+ + Seokhyun + Yoon + + + + + + SRP502899 + PRJNA1102362 + GSE264408 + + + Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS + + In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis. Overall design: We conducted single-cell RNA sequencing (scRNA-Seq) using Chromium (10X Genomics) on samples from 3 healthy mouse colons, 3 mouse colons with acute colitis induced by DSS, and 4 mouse colons with chronic colitis induced by DSS. + GSE264408 + + + + + pubmed + 38879692 + + + + + + + SRS21074410 + SAMN41019963 + GSM8217725 + + Mouse colon, Healthy1 + + 10090 + Mus musculus + + + + + bioproject + 1102362 + + + + + + + source_name + colon + + + tissue + colon + + + disease state + Healthy + + + treatment + sterile distilled water + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21074410 + SAMN41019963 + GSM8217725 + + + + + + + SRR28746900 + GSM8217725_r1 + + + + GSM8217725_r1 + + + + + loader + fastq-load.py + + + + + + SRS21074410 + SAMN41019963 + GSM8217725 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE266033.xml b/tests/data/GSE266033.xml new file mode 100644 index 0000000..9cfb741 --- /dev/null +++ b/tests/data/GSE266033.xml @@ -0,0 +1,4026 @@ + + + + + + + SRX24385260 + GSM8239685_r1 + + GSM8239685: 28.5 5xFAD MCAO; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141415 + GSM8239685 + + + + GSM8239685 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141415 + SAMN41101370 + GSM8239685 + + 28.5 5xFAD MCAO + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + ipsilateral + + + Sex + male + + + age + 12 months old + + + genotype + 5xFAD + + + treatment + MCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141415 + SAMN41101370 + GSM8239685 + + + + + + + SRR28822292 + GSM8239685_r1 + + + + GSM8239685_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=285aRE135LH-HetLH_S4_L001_R1_001.fastq.gz --read2PairFiles=285aRE135LH-HetLH_S4_L001_R2_001.fastq.gz --read3PairFiles=285aRE135LH-HetLH_S4_L001_I1_001.fastq.gz --read4PairFiles=285aRE135LH-HetLH_S4_L001_I2_001.fastq.gz + + + + + + SRS21141415 + SAMN41101370 + GSM8239685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822293 + GSM8239685_r2 + + + + GSM8239685_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=285aRE135LH-HetLH_S4_L002_R1_001.fastq.gz --read2PairFiles=285aRE135LH-HetLH_S4_L002_R2_001.fastq.gz --read3PairFiles=285aRE135LH-HetLH_S4_L002_I1_001.fastq.gz --read4PairFiles=285aRE135LH-HetLH_S4_L002_I2_001.fastq.gz + + + + + + SRS21141415 + SAMN41101370 + GSM8239685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385259 + GSM8239687_r1 + + GSM8239687: 29.4 5xFAD MCAO; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141414 + GSM8239687 + + + + GSM8239687 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + 29.4 5xFAD MCAO + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + ipsilateral + + + Sex + female + + + age + 12 months old + + + genotype + 5xFAD + + + treatment + MCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + + + + + + SRR28822294 + GSM8239687_r1 + + + + GSM8239687_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETLH_S4_L001_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETLH_S4_L001_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETLH_S4_L001_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETLH_S4_L001_I2_001.fastq.gz + + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822295 + GSM8239687_r2 + + + + GSM8239687_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETLH_S4_L002_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETLH_S4_L002_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETLH_S4_L002_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETLH_S4_L002_I2_001.fastq.gz + + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822296 + GSM8239687_r3 + + + + GSM8239687_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETLH_S4_L003_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETLH_S4_L003_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETLH_S4_L003_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETLH_S4_L003_I2_001.fastq.gz + + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822297 + GSM8239687_r4 + + + + GSM8239687_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETLH_S4_L004_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETLH_S4_L004_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETLH_S4_L004_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETLH_S4_L004_I2_001.fastq.gz + + + + + + SRS21141414 + SAMN41101368 + GSM8239687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385258 + GSM8239686_r1 + + GSM8239686: 29.4 5xFAD Sham; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141413 + GSM8239686 + + + + GSM8239686 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + 29.4 5xFAD Sham + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + contralateral + + + Sex + female + + + age + 12 months old + + + genotype + 5xFAD + + + treatment + Sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + + + + + + SRR28822298 + GSM8239686_r1 + + + + GSM8239686_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETRH_S3_L001_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETRH_S3_L001_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETRH_S3_L001_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETRH_S3_L001_I2_001.fastq.gz + + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822299 + GSM8239686_r2 + + + + GSM8239686_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETRH_S3_L002_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETRH_S3_L002_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETRH_S3_L002_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETRH_S3_L002_I2_001.fastq.gz + + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822300 + GSM8239686_r3 + + + + GSM8239686_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETRH_S3_L003_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETRH_S3_L003_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETRH_S3_L003_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETRH_S3_L003_I2_001.fastq.gz + + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822301 + GSM8239686_r4 + + + + GSM8239686_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=294bLELE-143HETRH_S3_L004_R1_001.fastq.gz --read2PairFiles=294bLELE-143HETRH_S3_L004_R2_001.fastq.gz --read3PairFiles=294bLELE-143HETRH_S3_L004_I1_001.fastq.gz --read4PairFiles=294bLELE-143HETRH_S3_L004_I2_001.fastq.gz + + + + + + SRS21141413 + SAMN41101369 + GSM8239686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385257 + GSM8239684_r1 + + GSM8239684: 28.5 5xFAD Sham; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141412 + GSM8239684 + + + + GSM8239684 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141412 + SAMN41101371 + GSM8239684 + + 28.5 5xFAD Sham + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + contralateral + + + Sex + male + + + age + 12 months old + + + genotype + 5xFAD + + + treatment + Sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141412 + SAMN41101371 + GSM8239684 + + + + + + + SRR28822302 + GSM8239684_r1 + + + + GSM8239684_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=285aRE135RH-HetRH_S3_L001_R1_001.fastq.gz --read2PairFiles=285aRE135RH-HetRH_S3_L001_R2_001.fastq.gz --read3PairFiles=285aRE135RH-HetRH_S3_L001_I1_001.fastq.gz --read4PairFiles=285aRE135RH-HetRH_S3_L001_I2_001.fastq.gz + + + + + + SRS21141412 + SAMN41101371 + GSM8239684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822307 + GSM8239684_r2 + + + + GSM8239684_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=285aRE135RH-HetRH_S3_L002_R1_001.fastq.gz --read2PairFiles=285aRE135RH-HetRH_S3_L002_R2_001.fastq.gz --read3PairFiles=285aRE135RH-HetRH_S3_L002_I1_001.fastq.gz --read4PairFiles=285aRE135RH-HetRH_S3_L002_I2_001.fastq.gz + + + + + + SRS21141412 + SAMN41101371 + GSM8239684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385256 + GSM8239682_r1 + + GSM8239682: 28.2 WT Sham; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141411 + GSM8239682 + + + + GSM8239682 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141411 + SAMN41101373 + GSM8239682 + + 28.2 WT Sham + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + ipsilateral + + + Sex + female + + + age + 12 months old + + + genotype + WT + + + treatment + Sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141411 + SAMN41101373 + GSM8239682 + + + + + + + SRR28822303 + GSM8239682_r1 + + + + GSM8239682_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=282bRE132RH-1117RH_S1_L001_R1_001.fastq.gz --read2PairFiles=282bRE132RH-1117RH_S1_L001_R2_001.fastq.gz --read3PairFiles=282bRE132RH-1117RH_S1_L001_I1_001.fastq.gz --read4PairFiles=282bRE132RH-1117RH_S1_L001_I2_001.fastq.gz + + + + + + SRS21141411 + SAMN41101373 + GSM8239682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822304 + GSM8239682_r2 + + + + GSM8239682_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=282bRE132RH-1117RH_S1_L002_R1_001.fastq.gz --read2PairFiles=282bRE132RH-1117RH_S1_L002_R2_001.fastq.gz --read3PairFiles=282bRE132RH-1117RH_S1_L002_I1_001.fastq.gz --read4PairFiles=282bRE132RH-1117RH_S1_L002_I2_001.fastq.gz + + + + + + SRS21141411 + SAMN41101373 + GSM8239682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385255 + GSM8239683_r1 + + GSM8239683: 28.2 WT MCAO; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141410 + GSM8239683 + + + + GSM8239683 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141410 + SAMN41101372 + GSM8239683 + + 28.2 WT MCAO + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + contralateral + + + Sex + female + + + age + 12 months old + + + genotype + WT + + + treatment + MCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141410 + SAMN41101372 + GSM8239683 + + + + + + + SRR28822305 + GSM8239683_r1 + + + + GSM8239683_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=282bRE132LH-1117LH_S2_L001_R1_001.fastq.gz --read2PairFiles=282bRE132LH-1117LH_S2_L001_R2_001.fastq.gz --read3PairFiles=282bRE132LH-1117LH_S2_L001_I1_001.fastq.gz --read4PairFiles=282bRE132LH-1117LH_S2_L001_I2_001.fastq.gz + + + + + + SRS21141410 + SAMN41101372 + GSM8239683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822306 + GSM8239683_r2 + + + + GSM8239683_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=282bRE132LH-1117LH_S2_L002_R1_001.fastq.gz --read2PairFiles=282bRE132LH-1117LH_S2_L002_R2_001.fastq.gz --read3PairFiles=282bRE132LH-1117LH_S2_L002_I1_001.fastq.gz --read4PairFiles=282bRE132LH-1117LH_S2_L002_I2_001.fastq.gz + + + + + + SRS21141410 + SAMN41101372 + GSM8239683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385254 + GSM8239681_r1 + + GSM8239681: 28.8 WT MCAO; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141409 + GSM8239681 + + + + GSM8239681 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + 28.8 WT MCAO + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + ipsilateral + + + Sex + male + + + age + 12 months old + + + genotype + WT + + + treatment + MCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + + + + + + SRR28822308 + GSM8239681_r1 + + + + GSM8239681_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139LH_S2_L001_R1_001.fastq.gz --read2PairFiles=288aLERE-139LH_S2_L001_R2_001.fastq.gz --read3PairFiles=288aLERE-139LH_S2_L001_I1_001.fastq.gz --read4PairFiles=288aLERE-139LH_S2_L001_I2_001.fastq.gz + + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822309 + GSM8239681_r2 + + + + GSM8239681_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139LH_S2_L002_R1_001.fastq.gz --read2PairFiles=288aLERE-139LH_S2_L002_R2_001.fastq.gz --read3PairFiles=288aLERE-139LH_S2_L002_I1_001.fastq.gz --read4PairFiles=288aLERE-139LH_S2_L002_I2_001.fastq.gz + + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822310 + GSM8239681_r3 + + + + GSM8239681_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139LH_S2_L003_R1_001.fastq.gz --read2PairFiles=288aLERE-139LH_S2_L003_R2_001.fastq.gz --read3PairFiles=288aLERE-139LH_S2_L003_I1_001.fastq.gz --read4PairFiles=288aLERE-139LH_S2_L003_I2_001.fastq.gz + + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822311 + GSM8239681_r4 + + + + GSM8239681_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139LH_S2_L004_R1_001.fastq.gz --read2PairFiles=288aLERE-139LH_S2_L004_R2_001.fastq.gz --read3PairFiles=288aLERE-139LH_S2_L004_I1_001.fastq.gz --read4PairFiles=288aLERE-139LH_S2_L004_I2_001.fastq.gz + + + + + + SRS21141409 + SAMN41101374 + GSM8239681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385253 + GSM8239680_r1 + + GSM8239680: 28.8 WT Sham; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141408 + GSM8239680 + + + + GSM8239680 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + 28.8 WT Sham + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + contralateral + + + Sex + male + + + age + 12 months old + + + genotype + WT + + + treatment + Sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + + + + + + SRR28822312 + GSM8239680_r1 + + + + GSM8239680_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139RH_S1_L001_R1_001.fastq.gz --read2PairFiles=288aLERE-139RH_S1_L001_R2_001.fastq.gz --read3PairFiles=288aLERE-139RH_S1_L001_I1_001.fastq.gz --read4PairFiles=288aLERE-139RH_S1_L001_I2_001.fastq.gz + + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822313 + GSM8239680_r2 + + + + GSM8239680_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139RH_S1_L002_R1_001.fastq.gz --read2PairFiles=288aLERE-139RH_S1_L002_R2_001.fastq.gz --read3PairFiles=288aLERE-139RH_S1_L002_I1_001.fastq.gz --read4PairFiles=288aLERE-139RH_S1_L002_I2_001.fastq.gz + + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822314 + GSM8239680_r3 + + + + GSM8239680_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139RH_S1_L003_R1_001.fastq.gz --read2PairFiles=288aLERE-139RH_S1_L003_R2_001.fastq.gz --read3PairFiles=288aLERE-139RH_S1_L003_I1_001.fastq.gz --read4PairFiles=288aLERE-139RH_S1_L003_I2_001.fastq.gz + + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822315 + GSM8239680_r4 + + + + GSM8239680_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=288aLERE-139RH_S1_L004_R1_001.fastq.gz --read2PairFiles=288aLERE-139RH_S1_L004_R2_001.fastq.gz --read3PairFiles=288aLERE-139RH_S1_L004_I1_001.fastq.gz --read4PairFiles=288aLERE-139RH_S1_L004_I2_001.fastq.gz + + + + + + SRS21141408 + SAMN41101375 + GSM8239680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385252 + GSM8239679_r1 + + GSM8239679: 25.4 WT MCAO; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141407 + GSM8239679 + + + + GSM8239679 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + 25.4 WT MCAO + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + ipsilateral + + + Sex + female + + + age + 12 months old + + + genotype + WT + + + treatment + MCAO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + + + + + + SRR28822316 + GSM8239679_r1 + + + + GSM8239679_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTLH_S6_L001_R1_001.fastq.gz --read2PairFiles=254bRE-129WTLH_S6_L001_R2_001.fastq.gz --read3PairFiles=254bRE-129WTLH_S6_L001_I1_001.fastq.gz --read4PairFiles=254bRE-129WTLH_S6_L001_I2_001.fastq.gz + + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822317 + GSM8239679_r2 + + + + GSM8239679_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTLH_S6_L002_R1_001.fastq.gz --read2PairFiles=254bRE-129WTLH_S6_L002_R2_001.fastq.gz --read3PairFiles=254bRE-129WTLH_S6_L002_I1_001.fastq.gz --read4PairFiles=254bRE-129WTLH_S6_L002_I2_001.fastq.gz + + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822318 + GSM8239679_r3 + + + + GSM8239679_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTLH_S6_L003_R1_001.fastq.gz --read2PairFiles=254bRE-129WTLH_S6_L003_R2_001.fastq.gz --read3PairFiles=254bRE-129WTLH_S6_L003_I1_001.fastq.gz --read4PairFiles=254bRE-129WTLH_S6_L003_I2_001.fastq.gz + + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822319 + GSM8239679_r4 + + + + GSM8239679_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTLH_S6_L004_R1_001.fastq.gz --read2PairFiles=254bRE-129WTLH_S6_L004_R2_001.fastq.gz --read3PairFiles=254bRE-129WTLH_S6_L004_I1_001.fastq.gz --read4PairFiles=254bRE-129WTLH_S6_L004_I2_001.fastq.gz + + + + + + SRS21141407 + SAMN41101376 + GSM8239679 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24385251 + GSM8239678_r1 + + GSM8239678: 25.4 WT Sham; Mus musculus; RNA-Seq + + + SRP504411 + PRJNA1105371 + + + + + + + SRS21141406 + GSM8239678 + + + + GSM8239678 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer's instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC. After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions. The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide. Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1854256 + SUB14407051 + + + + University of Miami + +
+ 1501 NW 10th Ave, BRB 711 + Miami + Florida + USA +
+ + Luisa + Cimmino + + + + + + SRP504411 + PRJNA1105371 + GSE266033 + + + Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke + + Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA. Overall design: The hippocampus of 5xFAD or WT mice was isolated 7 days post-stroke. The contralateral and ipsilateral side were collected on ice in Hibernate A medium and homogenized into a single cell suspension for analysis using scRNA-seq. + GSE266033 + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + 25.4 WT Sham + + 10090 + Mus musculus + + + + + bioproject + 1105371 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + hemisphere + contralateral + + + Sex + female + + + age + 12 months old + + + genotype + WT + + + treatment + Sham + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + + + + + + SRR28822320 + GSM8239678_r1 + + + + GSM8239678_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTRH_S5_L001_R1_001.fastq.gz --read2PairFiles=254bRE-129WTRH_S5_L001_R2_001.fastq.gz --read3PairFiles=254bRE-129WTRH_S5_L001_I1_001.fastq.gz --read4PairFiles=254bRE-129WTRH_S5_L001_I2_001.fastq.gz + + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822321 + GSM8239678_r2 + + + + GSM8239678_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTRH_S5_L002_R1_001.fastq.gz --read2PairFiles=254bRE-129WTRH_S5_L002_R2_001.fastq.gz --read3PairFiles=254bRE-129WTRH_S5_L002_I1_001.fastq.gz --read4PairFiles=254bRE-129WTRH_S5_L002_I2_001.fastq.gz + + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822322 + GSM8239678_r3 + + + + GSM8239678_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTRH_S5_L003_R1_001.fastq.gz --read2PairFiles=254bRE-129WTRH_S5_L003_R2_001.fastq.gz --read3PairFiles=254bRE-129WTRH_S5_L003_I1_001.fastq.gz --read4PairFiles=254bRE-129WTRH_S5_L003_I2_001.fastq.gz + + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR28822323 + GSM8239678_r4 + + + + GSM8239678_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=BBTT --read1PairFiles=254bRE-129WTRH_S5_L004_R1_001.fastq.gz --read2PairFiles=254bRE-129WTRH_S5_L004_R2_001.fastq.gz --read3PairFiles=254bRE-129WTRH_S5_L004_I1_001.fastq.gz --read4PairFiles=254bRE-129WTRH_S5_L004_I2_001.fastq.gz + + + + + + SRS21141406 + SAMN41101377 + GSM8239678 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE267764.xml b/tests/data/GSE267764.xml new file mode 100644 index 0000000..5d0b520 --- /dev/null +++ b/tests/data/GSE267764.xml @@ -0,0 +1,1200 @@ + + + + + + + SRX24593400 + GSM8275375_r1 + + GSM8275375: cKO2_cortex; Mus musculus; RNA-Seq + + + SRP508373 + PRJNA1112818 + + + + + + + SRS21331491 + GSM8275375 + + + + GSM8275375 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cell suspensions are handed off to the Broad Clinical Labs Single Cell processing team. Appropriate volume adjustments are made to ensure thetarget cell recoveryis met prior to the addition of reverse transcription mastermix. The cells in mastermix are then added to the 10x chip G along with 10x gel beads and partitioning oil. The chip is run on the 10x Chromium Controller to create an emulsion of single cells, RT mastermix and a barcoded gel bead. After emulsions are created, samples are immediately put on reverse transcription thermalcycler protocol set at 53OC for 45 minutes, 85OC for 5 minutes before holding at 4OC. The emulsion is then broken, and debris is removed via a Silane bead cleanup. The purified cDNA is then amplified with the following PCR conditions: Initial denaturation at 98°C for 3 minutes, followed by12 cyclesof denaturation at 98°C for 15 seconds, annealing at 63°C for 20 seconds, and extension at 72°C for 1 minute. A 0.6X SPRI cleanup is performed before being quanted on a Qubit. cDNA library construction is run on an entirely automated workflow. The cDNA is fragmented and repaired with the addition of an A-tail at 32OC for 5 minutes then 65OC for 30 minutes. A 0.8X double sided SPRI cleanup then removes undesired fragments. Adapters are ligated onto the DNA at 20OC for 15 minutes followed by a 0.8X SPRI. 10x dual indexed barcodes are added before a PCR reaction with the following conditions: An initial denaturation at 98°C for 45 seconds, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 20 seconds. These libraries undergo a final 0.8X double sided SPRI cleanup for size selection. Following PCR Cleanup, quality is confirmed using Quant-iT PicoGreen and an Agilent TapeStation to confirm library size. Samples are pooled together to accommodate the desired reads per cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1869270 + SUB14456115 + + + + Brigham and Women's Hospital + +
+ 221 Longwood Avenue, EBRC 3rd Floor + BOSTON + MASSACHUSETTS + USA +
+ + Jeong-Mi + Lee + + + + + + SRP508373 + PRJNA1112818 + GSE267764 + + + Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer's disease pathology [scRNA-Seq] + + Microglia, resident immune cells in the brain, play a critical role in neurodevelopment and neurological diseases. We investigated the role of the immune checkpoint molecule Tim-3 (Havcr2), which was recently identified as a genetic risk factor for late-onset Alzheimer's disease (LOAD) in microglia. While Tim-3 has been shown to play an important role in inducing T cell exhaustion, it shows high and specific expression in the microglia where its role is unknown. Here we show that Tim-3 expression in microglia was induced by TGFß signaling. Mechanistically, Tim-3 binds both Smad2 and Tgfbr2 by its C-terminus tail and enhances TGFß signaling by promoting the phosphorylation of Smad2 by Tgfbr, thereby contributing to microglial homeostasis. Genetic deletion of Tim-3 in microglia resulted in increased phagocytic activity with a gene expression profile skewed towards neurodegenerative microglia (MGnD) phenotype, also known as disease-associated microglia (DAM). Moreover, microglia-targeted deletion of Tim-3 ameliorated AD pathology in 5xFAD mice. Single-nucleus RNA sequencing (snRNA-seq) identified a subpopulation among MGnD/DAM microglia in Havcr2-deficient 5xFAD mice, characterized by increased pro-phagocytic and anti-inflammatory gene expression together with decreased proinflammatory gene expression. Additional single-cell RNAseq confirmed these transcriptomic shifts in Havcr2-deficient 5xFAD mice in most microglial clusters. Our study shows a Tim-3-mediated regulatory mechanism of homeostatic microglia through its interaction with TGFß signaling and the beneficial role of targeting microglial Tim-3 in AD mice. Our findings promise a potential therapeutic strategy targeting checkpoint molecule Tim-3 in currently intractable AD. Overall design: Female Tim3 f/f, 5XFAD and Tim3 f/f, CX3CR1 CreERT2, 5XFAD mice were prepared. Tamoxifen (150 mg/kg body weight) was injected intraperitoneally in two consecutive days at the age of 6 weeks. Microglia were isolated from the brain cortex at the age of 5 months. Mice were deeply anesthetized with CO2 and transcardially perfused with cold HBSS (Gibco). The brains were quickly removed from the skull into cold HBSS. The brain cortices were gently separated with forceps on ice under the microscope. The prepared cortices were homogenized gently with Dounce Homogenizer (Bellco Glass) on ice. After centrifugation, the pellet was dissolved in 70% Percoll Plus (GE Healthcare) solution, with 37% Percoll Plus put gently on top of it. After gentle centrifugation, the cell layer in the middle was collected into cold PBS-based flow cytometry (FCM) buffer, including 0.5% BSA and 2mM EDTA. The sorted microglia were then collected into PBS with 1% BSA. + GSE267764 + + + + + pubmed + 40205047 + + + + + + parent_bioproject + PRJNA926114 + + + + + + SRS21331491 + SAMN41437693 + GSM8275375 + + cKO2_cortex + + 10090 + Mus musculus + + + + + bioproject + 1112818 + + + + + + + source_name + Brain + + + tissue + Brain + + + Sex + female + + + cell type + Microglia + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21331491 + SAMN41437693 + GSM8275375 + + + + + + + SRR29069009 + GSM8275375_r1 + + + + GSM8275375_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331491 + SAMN41437693 + GSM8275375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29069010 + GSM8275375_r2 + + + + GSM8275375_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331491 + SAMN41437693 + GSM8275375 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24593399 + GSM8275374_r1 + + GSM8275374: cKO1_cortex; Mus musculus; RNA-Seq + + + SRP508373 + PRJNA1112818 + + + + + + + SRS21331489 + GSM8275374 + + + + GSM8275374 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cell suspensions are handed off to the Broad Clinical Labs Single Cell processing team. Appropriate volume adjustments are made to ensure thetarget cell recoveryis met prior to the addition of reverse transcription mastermix. The cells in mastermix are then added to the 10x chip G along with 10x gel beads and partitioning oil. The chip is run on the 10x Chromium Controller to create an emulsion of single cells, RT mastermix and a barcoded gel bead. After emulsions are created, samples are immediately put on reverse transcription thermalcycler protocol set at 53OC for 45 minutes, 85OC for 5 minutes before holding at 4OC. The emulsion is then broken, and debris is removed via a Silane bead cleanup. The purified cDNA is then amplified with the following PCR conditions: Initial denaturation at 98°C for 3 minutes, followed by12 cyclesof denaturation at 98°C for 15 seconds, annealing at 63°C for 20 seconds, and extension at 72°C for 1 minute. A 0.6X SPRI cleanup is performed before being quanted on a Qubit. cDNA library construction is run on an entirely automated workflow. The cDNA is fragmented and repaired with the addition of an A-tail at 32OC for 5 minutes then 65OC for 30 minutes. A 0.8X double sided SPRI cleanup then removes undesired fragments. Adapters are ligated onto the DNA at 20OC for 15 minutes followed by a 0.8X SPRI. 10x dual indexed barcodes are added before a PCR reaction with the following conditions: An initial denaturation at 98°C for 45 seconds, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 20 seconds. These libraries undergo a final 0.8X double sided SPRI cleanup for size selection. Following PCR Cleanup, quality is confirmed using Quant-iT PicoGreen and an Agilent TapeStation to confirm library size. Samples are pooled together to accommodate the desired reads per cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1869270 + SUB14456115 + + + + Brigham and Women's Hospital + +
+ 221 Longwood Avenue, EBRC 3rd Floor + BOSTON + MASSACHUSETTS + USA +
+ + Jeong-Mi + Lee + + + + + + SRP508373 + PRJNA1112818 + GSE267764 + + + Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer's disease pathology [scRNA-Seq] + + Microglia, resident immune cells in the brain, play a critical role in neurodevelopment and neurological diseases. We investigated the role of the immune checkpoint molecule Tim-3 (Havcr2), which was recently identified as a genetic risk factor for late-onset Alzheimer's disease (LOAD) in microglia. While Tim-3 has been shown to play an important role in inducing T cell exhaustion, it shows high and specific expression in the microglia where its role is unknown. Here we show that Tim-3 expression in microglia was induced by TGFß signaling. Mechanistically, Tim-3 binds both Smad2 and Tgfbr2 by its C-terminus tail and enhances TGFß signaling by promoting the phosphorylation of Smad2 by Tgfbr, thereby contributing to microglial homeostasis. Genetic deletion of Tim-3 in microglia resulted in increased phagocytic activity with a gene expression profile skewed towards neurodegenerative microglia (MGnD) phenotype, also known as disease-associated microglia (DAM). Moreover, microglia-targeted deletion of Tim-3 ameliorated AD pathology in 5xFAD mice. Single-nucleus RNA sequencing (snRNA-seq) identified a subpopulation among MGnD/DAM microglia in Havcr2-deficient 5xFAD mice, characterized by increased pro-phagocytic and anti-inflammatory gene expression together with decreased proinflammatory gene expression. Additional single-cell RNAseq confirmed these transcriptomic shifts in Havcr2-deficient 5xFAD mice in most microglial clusters. Our study shows a Tim-3-mediated regulatory mechanism of homeostatic microglia through its interaction with TGFß signaling and the beneficial role of targeting microglial Tim-3 in AD mice. Our findings promise a potential therapeutic strategy targeting checkpoint molecule Tim-3 in currently intractable AD. Overall design: Female Tim3 f/f, 5XFAD and Tim3 f/f, CX3CR1 CreERT2, 5XFAD mice were prepared. Tamoxifen (150 mg/kg body weight) was injected intraperitoneally in two consecutive days at the age of 6 weeks. Microglia were isolated from the brain cortex at the age of 5 months. Mice were deeply anesthetized with CO2 and transcardially perfused with cold HBSS (Gibco). The brains were quickly removed from the skull into cold HBSS. The brain cortices were gently separated with forceps on ice under the microscope. The prepared cortices were homogenized gently with Dounce Homogenizer (Bellco Glass) on ice. After centrifugation, the pellet was dissolved in 70% Percoll Plus (GE Healthcare) solution, with 37% Percoll Plus put gently on top of it. After gentle centrifugation, the cell layer in the middle was collected into cold PBS-based flow cytometry (FCM) buffer, including 0.5% BSA and 2mM EDTA. The sorted microglia were then collected into PBS with 1% BSA. + GSE267764 + + + + + pubmed + 40205047 + + + + + + parent_bioproject + PRJNA926114 + + + + + + SRS21331489 + SAMN41437694 + GSM8275374 + + cKO1_cortex + + 10090 + Mus musculus + + + + + bioproject + 1112818 + + + + + + + source_name + Brain + + + tissue + Brain + + + Sex + female + + + cell type + Microglia + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21331489 + SAMN41437694 + GSM8275374 + + + + + + + SRR29069011 + GSM8275374_r1 + + + + GSM8275374_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331489 + SAMN41437694 + GSM8275374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29069012 + GSM8275374_r2 + + + + GSM8275374_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331489 + SAMN41437694 + GSM8275374 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24593398 + GSM8275373_r1 + + GSM8275373: con2_cortex; Mus musculus; RNA-Seq + + + SRP508373 + PRJNA1112818 + + + + + + + SRS21331488 + GSM8275373 + + + + GSM8275373 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cell suspensions are handed off to the Broad Clinical Labs Single Cell processing team. Appropriate volume adjustments are made to ensure thetarget cell recoveryis met prior to the addition of reverse transcription mastermix. The cells in mastermix are then added to the 10x chip G along with 10x gel beads and partitioning oil. The chip is run on the 10x Chromium Controller to create an emulsion of single cells, RT mastermix and a barcoded gel bead. After emulsions are created, samples are immediately put on reverse transcription thermalcycler protocol set at 53OC for 45 minutes, 85OC for 5 minutes before holding at 4OC. The emulsion is then broken, and debris is removed via a Silane bead cleanup. The purified cDNA is then amplified with the following PCR conditions: Initial denaturation at 98°C for 3 minutes, followed by12 cyclesof denaturation at 98°C for 15 seconds, annealing at 63°C for 20 seconds, and extension at 72°C for 1 minute. A 0.6X SPRI cleanup is performed before being quanted on a Qubit. cDNA library construction is run on an entirely automated workflow. The cDNA is fragmented and repaired with the addition of an A-tail at 32OC for 5 minutes then 65OC for 30 minutes. A 0.8X double sided SPRI cleanup then removes undesired fragments. Adapters are ligated onto the DNA at 20OC for 15 minutes followed by a 0.8X SPRI. 10x dual indexed barcodes are added before a PCR reaction with the following conditions: An initial denaturation at 98°C for 45 seconds, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 20 seconds. These libraries undergo a final 0.8X double sided SPRI cleanup for size selection. Following PCR Cleanup, quality is confirmed using Quant-iT PicoGreen and an Agilent TapeStation to confirm library size. Samples are pooled together to accommodate the desired reads per cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1869270 + SUB14456115 + + + + Brigham and Women's Hospital + +
+ 221 Longwood Avenue, EBRC 3rd Floor + BOSTON + MASSACHUSETTS + USA +
+ + Jeong-Mi + Lee + + + + + + SRP508373 + PRJNA1112818 + GSE267764 + + + Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer's disease pathology [scRNA-Seq] + + Microglia, resident immune cells in the brain, play a critical role in neurodevelopment and neurological diseases. We investigated the role of the immune checkpoint molecule Tim-3 (Havcr2), which was recently identified as a genetic risk factor for late-onset Alzheimer's disease (LOAD) in microglia. While Tim-3 has been shown to play an important role in inducing T cell exhaustion, it shows high and specific expression in the microglia where its role is unknown. Here we show that Tim-3 expression in microglia was induced by TGFß signaling. Mechanistically, Tim-3 binds both Smad2 and Tgfbr2 by its C-terminus tail and enhances TGFß signaling by promoting the phosphorylation of Smad2 by Tgfbr, thereby contributing to microglial homeostasis. Genetic deletion of Tim-3 in microglia resulted in increased phagocytic activity with a gene expression profile skewed towards neurodegenerative microglia (MGnD) phenotype, also known as disease-associated microglia (DAM). Moreover, microglia-targeted deletion of Tim-3 ameliorated AD pathology in 5xFAD mice. Single-nucleus RNA sequencing (snRNA-seq) identified a subpopulation among MGnD/DAM microglia in Havcr2-deficient 5xFAD mice, characterized by increased pro-phagocytic and anti-inflammatory gene expression together with decreased proinflammatory gene expression. Additional single-cell RNAseq confirmed these transcriptomic shifts in Havcr2-deficient 5xFAD mice in most microglial clusters. Our study shows a Tim-3-mediated regulatory mechanism of homeostatic microglia through its interaction with TGFß signaling and the beneficial role of targeting microglial Tim-3 in AD mice. Our findings promise a potential therapeutic strategy targeting checkpoint molecule Tim-3 in currently intractable AD. Overall design: Female Tim3 f/f, 5XFAD and Tim3 f/f, CX3CR1 CreERT2, 5XFAD mice were prepared. Tamoxifen (150 mg/kg body weight) was injected intraperitoneally in two consecutive days at the age of 6 weeks. Microglia were isolated from the brain cortex at the age of 5 months. Mice were deeply anesthetized with CO2 and transcardially perfused with cold HBSS (Gibco). The brains were quickly removed from the skull into cold HBSS. The brain cortices were gently separated with forceps on ice under the microscope. The prepared cortices were homogenized gently with Dounce Homogenizer (Bellco Glass) on ice. After centrifugation, the pellet was dissolved in 70% Percoll Plus (GE Healthcare) solution, with 37% Percoll Plus put gently on top of it. After gentle centrifugation, the cell layer in the middle was collected into cold PBS-based flow cytometry (FCM) buffer, including 0.5% BSA and 2mM EDTA. The sorted microglia were then collected into PBS with 1% BSA. + GSE267764 + + + + + pubmed + 40205047 + + + + + + parent_bioproject + PRJNA926114 + + + + + + SRS21331488 + SAMN41437695 + GSM8275373 + + con2_cortex + + 10090 + Mus musculus + + + + + bioproject + 1112818 + + + + + + + source_name + Brain + + + tissue + Brain + + + Sex + female + + + cell type + Microglia + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21331488 + SAMN41437695 + GSM8275373 + + + + + + + SRR29069013 + GSM8275373_r1 + + + + GSM8275373_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331488 + SAMN41437695 + GSM8275373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29069014 + GSM8275373_r2 + + + + GSM8275373_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331488 + SAMN41437695 + GSM8275373 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24593397 + GSM8275372_r1 + + GSM8275372: con1_cortex; Mus musculus; RNA-Seq + + + SRP508373 + PRJNA1112818 + + + + + + + SRS21331487 + GSM8275372 + + + + GSM8275372 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Cell suspensions are handed off to the Broad Clinical Labs Single Cell processing team. Appropriate volume adjustments are made to ensure thetarget cell recoveryis met prior to the addition of reverse transcription mastermix. The cells in mastermix are then added to the 10x chip G along with 10x gel beads and partitioning oil. The chip is run on the 10x Chromium Controller to create an emulsion of single cells, RT mastermix and a barcoded gel bead. After emulsions are created, samples are immediately put on reverse transcription thermalcycler protocol set at 53OC for 45 minutes, 85OC for 5 minutes before holding at 4OC. The emulsion is then broken, and debris is removed via a Silane bead cleanup. The purified cDNA is then amplified with the following PCR conditions: Initial denaturation at 98°C for 3 minutes, followed by12 cyclesof denaturation at 98°C for 15 seconds, annealing at 63°C for 20 seconds, and extension at 72°C for 1 minute. A 0.6X SPRI cleanup is performed before being quanted on a Qubit. cDNA library construction is run on an entirely automated workflow. The cDNA is fragmented and repaired with the addition of an A-tail at 32OC for 5 minutes then 65OC for 30 minutes. A 0.8X double sided SPRI cleanup then removes undesired fragments. Adapters are ligated onto the DNA at 20OC for 15 minutes followed by a 0.8X SPRI. 10x dual indexed barcodes are added before a PCR reaction with the following conditions: An initial denaturation at 98°C for 45 seconds, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 20 seconds. These libraries undergo a final 0.8X double sided SPRI cleanup for size selection. Following PCR Cleanup, quality is confirmed using Quant-iT PicoGreen and an Agilent TapeStation to confirm library size. Samples are pooled together to accommodate the desired reads per cell. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1869270 + SUB14456115 + + + + Brigham and Women's Hospital + +
+ 221 Longwood Avenue, EBRC 3rd Floor + BOSTON + MASSACHUSETTS + USA +
+ + Jeong-Mi + Lee + + + + + + SRP508373 + PRJNA1112818 + GSE267764 + + + Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer's disease pathology [scRNA-Seq] + + Microglia, resident immune cells in the brain, play a critical role in neurodevelopment and neurological diseases. We investigated the role of the immune checkpoint molecule Tim-3 (Havcr2), which was recently identified as a genetic risk factor for late-onset Alzheimer's disease (LOAD) in microglia. While Tim-3 has been shown to play an important role in inducing T cell exhaustion, it shows high and specific expression in the microglia where its role is unknown. Here we show that Tim-3 expression in microglia was induced by TGFß signaling. Mechanistically, Tim-3 binds both Smad2 and Tgfbr2 by its C-terminus tail and enhances TGFß signaling by promoting the phosphorylation of Smad2 by Tgfbr, thereby contributing to microglial homeostasis. Genetic deletion of Tim-3 in microglia resulted in increased phagocytic activity with a gene expression profile skewed towards neurodegenerative microglia (MGnD) phenotype, also known as disease-associated microglia (DAM). Moreover, microglia-targeted deletion of Tim-3 ameliorated AD pathology in 5xFAD mice. Single-nucleus RNA sequencing (snRNA-seq) identified a subpopulation among MGnD/DAM microglia in Havcr2-deficient 5xFAD mice, characterized by increased pro-phagocytic and anti-inflammatory gene expression together with decreased proinflammatory gene expression. Additional single-cell RNAseq confirmed these transcriptomic shifts in Havcr2-deficient 5xFAD mice in most microglial clusters. Our study shows a Tim-3-mediated regulatory mechanism of homeostatic microglia through its interaction with TGFß signaling and the beneficial role of targeting microglial Tim-3 in AD mice. Our findings promise a potential therapeutic strategy targeting checkpoint molecule Tim-3 in currently intractable AD. Overall design: Female Tim3 f/f, 5XFAD and Tim3 f/f, CX3CR1 CreERT2, 5XFAD mice were prepared. Tamoxifen (150 mg/kg body weight) was injected intraperitoneally in two consecutive days at the age of 6 weeks. Microglia were isolated from the brain cortex at the age of 5 months. Mice were deeply anesthetized with CO2 and transcardially perfused with cold HBSS (Gibco). The brains were quickly removed from the skull into cold HBSS. The brain cortices were gently separated with forceps on ice under the microscope. The prepared cortices were homogenized gently with Dounce Homogenizer (Bellco Glass) on ice. After centrifugation, the pellet was dissolved in 70% Percoll Plus (GE Healthcare) solution, with 37% Percoll Plus put gently on top of it. After gentle centrifugation, the cell layer in the middle was collected into cold PBS-based flow cytometry (FCM) buffer, including 0.5% BSA and 2mM EDTA. The sorted microglia were then collected into PBS with 1% BSA. + GSE267764 + + + + + pubmed + 40205047 + + + + + + parent_bioproject + PRJNA926114 + + + + + + SRS21331487 + SAMN41437696 + GSM8275372 + + con1_cortex + + 10090 + Mus musculus + + + + + bioproject + 1112818 + + + + + + + source_name + Brain + + + tissue + Brain + + + Sex + female + + + cell type + Microglia + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21331487 + SAMN41437696 + GSM8275372 + + + + + + + SRR29069015 + GSM8275372_r1 + + + + GSM8275372_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331487 + SAMN41437696 + GSM8275372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR29069016 + GSM8275372_r2 + + + + GSM8275372_r1 + + + + + loader + fastq-load.py + + + + + + SRS21331487 + SAMN41437696 + GSM8275372 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE267933.xml b/tests/data/GSE267933.xml new file mode 100644 index 0000000..5dedf41 --- /dev/null +++ b/tests/data/GSE267933.xml @@ -0,0 +1,1312 @@ + + + + + + + SRX24614051 + GSM8281763_r1 + + GSM8281763: Hippocampus_Surgery_rep3; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351285 + GSM8281763 + + + + GSM8281763 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351285 + SAMN41463838 + GSM8281763 + + Hippocampus_Surgery_rep3 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351285 + SAMN41463838 + GSM8281763 + + + + + + + SRR29089909 + GSM8281763_r1 + + + + GSM8281763_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351285 + SAMN41463838 + GSM8281763 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX24614050 + GSM8281762_r1 + + GSM8281762: Hippocampus_Surgery_rep2; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351284 + GSM8281762 + + + + GSM8281762 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351284 + SAMN41463839 + GSM8281762 + + Hippocampus_Surgery_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351284 + SAMN41463839 + GSM8281762 + + + + + + + SRR29089910 + GSM8281762_r1 + + + + GSM8281762_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351284 + SAMN41463839 + GSM8281762 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX24614049 + GSM8281761_r1 + + GSM8281761: Hippocampus_Surgery_rep1; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351282 + GSM8281761 + + + + GSM8281761 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351282 + SAMN41463840 + GSM8281761 + + Hippocampus_Surgery_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351282 + SAMN41463840 + GSM8281761 + + + + + + + SRR29089911 + GSM8281761_r1 + + + + GSM8281761_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351282 + SAMN41463840 + GSM8281761 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX24614048 + GSM8281760_r1 + + GSM8281760: Hippocampus_Control_rep3; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351283 + GSM8281760 + + + + GSM8281760 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351283 + SAMN41463841 + GSM8281760 + + Hippocampus_Control_rep3 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351283 + SAMN41463841 + GSM8281760 + + + + + + + SRR29089912 + GSM8281760_r1 + + + + GSM8281760_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351283 + SAMN41463841 + GSM8281760 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX24614047 + GSM8281759_r1 + + GSM8281759: Hippocampus_Control_rep2; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351281 + GSM8281759 + + + + GSM8281759 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351281 + SAMN41463842 + GSM8281759 + + Hippocampus_Control_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351281 + SAMN41463842 + GSM8281759 + + + + + + + SRR29089913 + GSM8281759_r1 + + + + GSM8281759_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351281 + SAMN41463842 + GSM8281759 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX24614046 + GSM8281758_r1 + + GSM8281758: Hippocampus_Control_rep1; Mus musculus; RNA-Seq + + + SRP508801 + PRJNA1113658 + + + + + + + SRS21351280 + GSM8281758 + + + + GSM8281758 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis. scRNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing. + + + + + Illumina HiSeq 2500 + + + + + + SRA1871912 + SUB14463243 + + + + Chinese Academy of Medical Sciences and Peking Union Medical College + +
+ No.4 Jiang Wang Temple Street + Nanjing + China +
+ + Xiaoli + Min + + + + + + SRP508801 + PRJNA1113658 + GSE267933 + + + Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment + + This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline. Overall design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing. + GSE267933 + + + + + pubmed + 39540334 + + + + + + + SRS21351280 + SAMN41463843 + GSM8281758 + + Hippocampus_Control_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1113658 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21351280 + SAMN41463843 + GSM8281758 + + + + + + + SRR29089914 + GSM8281758_r1 + + + + GSM8281758_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21351280 + SAMN41463843 + GSM8281758 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE268343.xml b/tests/data/GSE268343.xml new file mode 100644 index 0000000..38ceab0 --- /dev/null +++ b/tests/data/GSE268343.xml @@ -0,0 +1,1264 @@ + + + + + + + SRX24696700 + GSM8289880_r1 + + GSM8289880: Camk2a-Vps13D KO, replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424233 + GSM8289880 + + + + GSM8289880 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424233 + SAMN41528163 + GSM8289880 + + Camk2a-Vps13D KO, replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Camk2a-Vps15D KO + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424233 + SAMN41528163 + GSM8289880 + + + + + + + SRR29176513 + GSM8289880_r1 + + + + GSM8289880_r1 + + + + + + SRS21424233 + SAMN41528163 + GSM8289880 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24696699 + GSM8289879_r1 + + GSM8289879: Camk2a-Vps13D KO, replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424232 + GSM8289879 + + + + GSM8289879 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424232 + SAMN41528164 + GSM8289879 + + Camk2a-Vps13D KO, replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Camk2a-Vps14D KO + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424232 + SAMN41528164 + GSM8289879 + + + + + + + SRR29176514 + GSM8289879_r1 + + + + GSM8289879_r1 + + + + + + SRS21424232 + SAMN41528164 + GSM8289879 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24696698 + GSM8289878_r1 + + GSM8289878: Camk2a-Vps13D KO, replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424231 + GSM8289878 + + + + GSM8289878 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424231 + SAMN41528165 + GSM8289878 + + Camk2a-Vps13D KO, replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Camk2a-Vps13D KO + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424231 + SAMN41528165 + GSM8289878 + + + + + + + SRR29176515 + GSM8289878_r1 + + + + GSM8289878_r1 + + + + + + SRS21424231 + SAMN41528165 + GSM8289878 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24696697 + GSM8289877_r1 + + GSM8289877: Wilt type, replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424230 + GSM8289877 + + + + GSM8289877 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424230 + SAMN41528166 + GSM8289877 + + Wilt type, replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Wilt type + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424230 + SAMN41528166 + GSM8289877 + + + + + + + SRR29176516 + GSM8289877_r1 + + + + GSM8289877_r1 + + + + + + SRS21424230 + SAMN41528166 + GSM8289877 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24696696 + GSM8289876_r1 + + GSM8289876: Wilt type, replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424229 + GSM8289876 + + + + GSM8289876 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424229 + SAMN41528167 + GSM8289876 + + Wilt type, replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Wilt type + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424229 + SAMN41528167 + GSM8289876 + + + + + + + SRR29176517 + GSM8289876_r1 + + + + GSM8289876_r1 + + + + + + SRS21424229 + SAMN41528167 + GSM8289876 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24696695 + GSM8289875_r1 + + GSM8289875: Wilt type, replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP509829 + PRJNA1116244 + + + + + + + SRS21424228 + GSM8289875 + + + + GSM8289875 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer's instructions. Library was performed accoding to the manufacturer's instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)). + + + + + Illumina NovaSeq X Plus + + + + + + SRA1877869 + SUB14477163 + + + + MCCB, UMass Chan + +
+ 164 Plantation St + Unionville + CT + USA +
+ + Haibo + Liu + + + + + + SRP509829 + PRJNA1116244 + GSE268343 + + + Gene expression profile at single cell level from hippocampus of wild type mice and Camk2a-Vps13D KO mice + + The failure to clear mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but the relationship and role of inflammation in these conditions is not fully understood.To investigate it, we established a model for neurodegeneration caused by mitochondrial impairment by removing Vps13D from the hippocampus.We use single cell RNA sequencing to analyze the gene expression profile of wild type mice and Camk2a-Vps13D KO mice. Overall design: Hippocampus single cell suspensions from wild type mice and Camk2a-Vps13D KO mice were used to generate scRNA-seq libraries with Chromium Next GEM Single Cell 3' Reagent Kits v3.1. + GSE268343 + + + + + pubmed + 40563011 + + + + + + + SRS21424228 + SAMN41528168 + GSM8289875 + + Wilt type, replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1116244 + + + + + + + source_name + Hippocampus + + + tissue + Hippocampus + + + cell line + none + + + cell type + neurons, glias, vascular cells, and other cells in the brain + + + genotype + Wilt type + + + treatment + none + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21424228 + SAMN41528168 + GSM8289875 + + + + + + + SRR29176518 + GSM8289875_r1 + + + + GSM8289875_r1 + + + + + + SRS21424228 + SAMN41528168 + GSM8289875 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE268642.xml b/tests/data/GSE268642.xml new file mode 100644 index 0000000..43193af --- /dev/null +++ b/tests/data/GSE268642.xml @@ -0,0 +1,1912 @@ + + + + + + + SRX24747081 + GSM8295842_r1 + + GSM8295842: HippoCortex_Young_EGFP_3; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468868 + GSM8295842 + + + + GSM8295842 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468868 + SAMN41595640 + GSM8295842 + + HippoCortex_Young_EGFP_3 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468868 + SAMN41595640 + GSM8295842 + + + + + + + SRR29228310 + GSM8295842_r1 + + + + GSM8295842_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468868 + SAMN41595640 + GSM8295842 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747080 + GSM8295841_r1 + + GSM8295841: HippoCortex_Young_EGFP_2; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468867 + GSM8295841 + + + + GSM8295841 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468867 + SAMN41595641 + GSM8295841 + + HippoCortex_Young_EGFP_2 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468867 + SAMN41595641 + GSM8295841 + + + + + + + SRR29228311 + GSM8295841_r1 + + + + GSM8295841_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468867 + SAMN41595641 + GSM8295841 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747079 + GSM8295840_r1 + + GSM8295840: HippoCortex_Young_EGFP_1; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468866 + GSM8295840 + + + + GSM8295840 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468866 + SAMN41595642 + GSM8295840 + + HippoCortex_Young_EGFP_1 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468866 + SAMN41595642 + GSM8295840 + + + + + + + SRR29228312 + GSM8295840_r1 + + + + GSM8295840_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468866 + SAMN41595642 + GSM8295840 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747078 + GSM8295839_r1 + + GSM8295839: HippoCortex_Aged_B3GNT3_3; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468865 + GSM8295839 + + + + GSM8295839 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468865 + SAMN41595643 + GSM8295839 + + HippoCortex_Aged_B3GNT3_3 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-B3GNT3 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468865 + SAMN41595643 + GSM8295839 + + + + + + + SRR29228313 + GSM8295839_r1 + + + + GSM8295839_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468865 + SAMN41595643 + GSM8295839 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747077 + GSM8295838_r1 + + GSM8295838: HippoCortex_Aged_B3GNT3_2; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468863 + GSM8295838 + + + + GSM8295838 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468863 + SAMN41595644 + GSM8295838 + + HippoCortex_Aged_B3GNT3_2 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-B3GNT3 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468863 + SAMN41595644 + GSM8295838 + + + + + + + SRR29228314 + GSM8295838_r1 + + + + GSM8295838_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468863 + SAMN41595644 + GSM8295838 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747076 + GSM8295837_r1 + + GSM8295837: HippoCortex_Aged_B3GNT3_1; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468864 + GSM8295837 + + + + GSM8295837 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468864 + SAMN41595645 + GSM8295837 + + HippoCortex_Aged_B3GNT3_1 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-B3GNT3 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468864 + SAMN41595645 + GSM8295837 + + + + + + + SRR29228315 + GSM8295837_r1 + + + + GSM8295837_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468864 + SAMN41595645 + GSM8295837 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747075 + GSM8295836_r1 + + GSM8295836: HippoCortex_Aged_EGFP_3; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468862 + GSM8295836 + + + + GSM8295836 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468862 + SAMN41595646 + GSM8295836 + + HippoCortex_Aged_EGFP_3 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468862 + SAMN41595646 + GSM8295836 + + + + + + + SRR29228316 + GSM8295836_r1 + + + + GSM8295836_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468862 + SAMN41595646 + GSM8295836 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747074 + GSM8295835_r1 + + GSM8295835: HippoCortex_Aged_EGFP_2; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468861 + GSM8295835 + + + + GSM8295835 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468861 + SAMN41595647 + GSM8295835 + + HippoCortex_Aged_EGFP_2 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468861 + SAMN41595647 + GSM8295835 + + + + + + + SRR29228317 + GSM8295835_r1 + + + + GSM8295835_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468861 + SAMN41595647 + GSM8295835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24747073 + GSM8295834_r1 + + GSM8295834: HippoCortex_Aged_EGFP_1; Mus musculus; RNA-Seq + + + SRP510722 + PRJNA1117950 + + + + + + + SRS21468860 + GSM8295834 + + + + GSM8295834 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS. Libraries were prepared using the Chromium Single Cell 3' Kit v3.1 (10X Genomics) according to the manufacturer's protocol, targeting 10,000 nuclei per sample. + + + + + Illumina NovaSeq X Plus + + + + + + SRA1883009 + SUB14490486 + + + + Stanford University + +
+ 279 Campus Dr + Stanford + CA + USA +
+ + Olivia + Gautier + + + + + + SRP510722 + PRJNA1117950 + GSE268642 + + + Overexpression of brain endothelial mucin-type O-glycan biosynthesis promotes brain homeostasis in aged mice + + In our study, we find that AAV-mediated brain endothelial B3GNT3 overexpression reduces neuroinflammatory markers and cognitive deficits in aged mice. Here, we perform snRNA-seq to characterize the cellular and molecular changes induced by brain endothelial B3GNT3 overexpression. Overall design: snRNA-sequencing of pooled cortical and hippocampal tissues from aged mice treated with AAV-EGFP, aged mice treated with AAV-B3GNT3, and young mice treated with AAV-EGFP + GSE268642 + + + + + pubmed + 40011765 + + + + + + + SRS21468860 + SAMN41595648 + GSM8295834 + + HippoCortex_Aged_EGFP_1 + + 10090 + Mus musculus + + + + + bioproject + 1117950 + + + + + + + source_name + Hippocampus and cortex + + + tissue + Hippocampus and cortex + + + genotype + WT + + + treatment + AAV-EGFP + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21468860 + SAMN41595648 + GSM8295834 + + + + + + + SRR29228318 + GSM8295834_r1 + + + + GSM8295834_r1 + + + + + loader + fastq-load.py + + + + + + SRS21468860 + SAMN41595648 + GSM8295834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE269499.xml b/tests/data/GSE269499.xml new file mode 100644 index 0000000..a4d2bdc --- /dev/null +++ b/tests/data/GSE269499.xml @@ -0,0 +1,6332 @@ + + + + + + + SRX24860546 + GSM8316817_r1 + + GSM8316817: 20778X6, WT Cerebellum, Social 10, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570578 + GSM8316817 + + + + GSM8316817 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570578 + SAMN41776188 + GSM8316817 + + 20778X6, WT Cerebellum, Social 10, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570578 + SAMN41776188 + GSM8316817 + + + + + + + SRR29344828 + GSM8316817_r1 + + + + GSM8316817_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570578 + SAMN41776188 + GSM8316817 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860545 + GSM8316816_r1 + + GSM8316816: 20778X4, WT Cerebellum, Social 10, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570576 + GSM8316816 + + + + GSM8316816 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570576 + SAMN41776189 + GSM8316816 + + 20778X4, WT Cerebellum, Social 10, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570576 + SAMN41776189 + GSM8316816 + + + + + + + SRR29344829 + GSM8316816_r1 + + + + GSM8316816_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570576 + SAMN41776189 + GSM8316816 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860544 + GSM8316815_r1 + + GSM8316815: 20778X2, WT Cerebellum, Social 10, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570577 + GSM8316815 + + + + GSM8316815 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570577 + SAMN41776190 + GSM8316815 + + 20778X2, WT Cerebellum, Social 10, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570577 + SAMN41776190 + GSM8316815 + + + + + + + SRR29344830 + GSM8316815_r1 + + + + GSM8316815_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570577 + SAMN41776190 + GSM8316815 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860543 + GSM8316814_r1 + + GSM8316814: 20053x6, WT Cerebellum, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570575 + GSM8316814 + + + + GSM8316814 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570575 + SAMN41776191 + GSM8316814 + + 20053x6, WT Cerebellum, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570575 + SAMN41776191 + GSM8316814 + + + + + + + SRR29344831 + GSM8316814_r1 + + + + GSM8316814_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570575 + SAMN41776191 + GSM8316814 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860542 + GSM8316813_r1 + + GSM8316813: 20053x5, WT Cerebellum, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570574 + GSM8316813 + + + + GSM8316813 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570574 + SAMN41776192 + GSM8316813 + + 20053x5, WT Cerebellum, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570574 + SAMN41776192 + GSM8316813 + + + + + + + SRR29344832 + GSM8316813_r1 + + + + GSM8316813_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570574 + SAMN41776192 + GSM8316813 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860541 + GSM8316812_r1 + + GSM8316812: 20053x4, WT Cerebellum, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570573 + GSM8316812 + + + + GSM8316812 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570573 + SAMN41776193 + GSM8316812 + + 20053x4, WT Cerebellum, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570573 + SAMN41776193 + GSM8316812 + + + + + + + SRR29344833 + GSM8316812_r1 + + + + GSM8316812_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570573 + SAMN41776193 + GSM8316812 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860540 + GSM8316811_r1 + + GSM8316811: 20053x3, WT Cerebellum, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570571 + GSM8316811 + + + + GSM8316811 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570571 + SAMN41776194 + GSM8316811 + + 20053x3, WT Cerebellum, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570571 + SAMN41776194 + GSM8316811 + + + + + + + SRR29344834 + GSM8316811_r1 + + + + GSM8316811_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570571 + SAMN41776194 + GSM8316811 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860539 + GSM8316810_r1 + + GSM8316810: 20053x2, WT Cerebellum, Not, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570572 + GSM8316810 + + + + GSM8316810 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570572 + SAMN41776195 + GSM8316810 + + 20053x2, WT Cerebellum, Not, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570572 + SAMN41776195 + GSM8316810 + + + + + + + SRR29344835 + GSM8316810_r1 + + + + GSM8316810_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570572 + SAMN41776195 + GSM8316810 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860538 + GSM8316809_r1 + + GSM8316809: 20053x1, WT Cerebellum, Social 35, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570570 + GSM8316809 + + + + GSM8316809 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570570 + SAMN41776196 + GSM8316809 + + 20053x1, WT Cerebellum, Social 35, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570570 + SAMN41776196 + GSM8316809 + + + + + + + SRR29344836 + GSM8316809_r1 + + + + GSM8316809_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570570 + SAMN41776196 + GSM8316809 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860537 + GSM8316808_r1 + + GSM8316808: 19957x2, WT Cerebellum, Social 35, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570569 + GSM8316808 + + + + GSM8316808 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570569 + SAMN41776197 + GSM8316808 + + 19957x2, WT Cerebellum, Social 35, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570569 + SAMN41776197 + GSM8316808 + + + + + + + SRR29344837 + GSM8316808_r1 + + + + GSM8316808_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570569 + SAMN41776197 + GSM8316808 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860536 + GSM8316807_r1 + + GSM8316807: 20523x4, WT Cerebellum, Not, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570568 + GSM8316807 + + + + GSM8316807 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570568 + SAMN41776198 + GSM8316807 + + 20523x4, WT Cerebellum, Not, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570568 + SAMN41776198 + GSM8316807 + + + + + + + SRR29344838 + GSM8316807_r1 + + + + GSM8316807_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570568 + SAMN41776198 + GSM8316807 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860535 + GSM8316806_r1 + + GSM8316806: 20521x4, WT Cerebellum, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570567 + GSM8316806 + + + + GSM8316806 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570567 + SAMN41776199 + GSM8316806 + + 20521x4, WT Cerebellum, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570567 + SAMN41776199 + GSM8316806 + + + + + + + SRR29344839 + GSM8316806_r1 + + + + GSM8316806_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570567 + SAMN41776199 + GSM8316806 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860534 + GSM8316805_r1 + + GSM8316805: 20375x10, WT Cerebellum, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570566 + GSM8316805 + + + + GSM8316805 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570566 + SAMN41776200 + GSM8316805 + + 20375x10, WT Cerebellum, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570566 + SAMN41776200 + GSM8316805 + + + + + + + SRR29344840 + GSM8316805_r1 + + + + GSM8316805_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570566 + SAMN41776200 + GSM8316805 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860533 + GSM8316804_r1 + + GSM8316804: 20251x3, WT Cerebellum, Social 35, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570565 + GSM8316804 + + + + GSM8316804 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570565 + SAMN41776201 + GSM8316804 + + 20251x3, WT Cerebellum, Social 35, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + Cerebellum + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570565 + SAMN41776201 + GSM8316804 + + + + + + + SRR29344841 + GSM8316804_r1 + + + + GSM8316804_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570565 + SAMN41776201 + GSM8316804 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860532 + GSM8316803_r1 + + GSM8316803: 20778X5, WT PFC, Social 10, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570564 + GSM8316803 + + + + GSM8316803 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570564 + SAMN41776202 + GSM8316803 + + 20778X5, WT PFC, Social 10, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570564 + SAMN41776202 + GSM8316803 + + + + + + + SRR29344842 + GSM8316803_r1 + + + + GSM8316803_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570564 + SAMN41776202 + GSM8316803 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860531 + GSM8316802_r1 + + GSM8316802: 20778X3, WT PFC, Social 10, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570563 + GSM8316802 + + + + GSM8316802 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570563 + SAMN41776203 + GSM8316802 + + 20778X3, WT PFC, Social 10, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570563 + SAMN41776203 + GSM8316802 + + + + + + + SRR29344843 + GSM8316802_r1 + + + + GSM8316802_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570563 + SAMN41776203 + GSM8316802 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860530 + GSM8316801_r1 + + GSM8316801: 20778X1, WT PFC, Social 10, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570562 + GSM8316801 + + + + GSM8316801 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570562 + SAMN41776204 + GSM8316801 + + 20778X1, WT PFC, Social 10, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 10 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570562 + SAMN41776204 + GSM8316801 + + + + + + + SRR29344844 + GSM8316801_r1 + + + + GSM8316801_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570562 + SAMN41776204 + GSM8316801 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860529 + GSM8316800_r1 + + GSM8316800: 20042x6, WT PFC, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570561 + GSM8316800 + + + + GSM8316800 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570561 + SAMN41776205 + GSM8316800 + + 20042x6, WT PFC, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570561 + SAMN41776205 + GSM8316800 + + + + + + + SRR29344845 + GSM8316800_r1 + + + + GSM8316800_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570561 + SAMN41776205 + GSM8316800 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860528 + GSM8316799_r1 + + GSM8316799: 20042x5, WT PFC, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570560 + GSM8316799 + + + + GSM8316799 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570560 + SAMN41776206 + GSM8316799 + + 20042x5, WT PFC, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570560 + SAMN41776206 + GSM8316799 + + + + + + + SRR29344846 + GSM8316799_r1 + + + + GSM8316799_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570560 + SAMN41776206 + GSM8316799 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860527 + GSM8316798_r1 + + GSM8316798: 20042x4, WT PFC, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570559 + GSM8316798 + + + + GSM8316798 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570559 + SAMN41776207 + GSM8316798 + + 20042x4, WT PFC, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570559 + SAMN41776207 + GSM8316798 + + + + + + + SRR29344847 + GSM8316798_r1 + + + + GSM8316798_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570559 + SAMN41776207 + GSM8316798 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860526 + GSM8316797_r1 + + GSM8316797: 20042x3, WT PFC, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570558 + GSM8316797 + + + + GSM8316797 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570558 + SAMN41776208 + GSM8316797 + + 20042x3, WT PFC, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570558 + SAMN41776208 + GSM8316797 + + + + + + + SRR29344848 + GSM8316797_r1 + + + + GSM8316797_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570558 + SAMN41776208 + GSM8316797 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860525 + GSM8316796_r1 + + GSM8316796: 20042x2, WT PFC, Not, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570557 + GSM8316796 + + + + GSM8316796 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570557 + SAMN41776209 + GSM8316796 + + 20042x2, WT PFC, Not, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570557 + SAMN41776209 + GSM8316796 + + + + + + + SRR29344849 + GSM8316796_r1 + + + + GSM8316796_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570557 + SAMN41776209 + GSM8316796 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860524 + GSM8316795_r1 + + GSM8316795: 20042x1, WT PFC, Social 35, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570556 + GSM8316795 + + + + GSM8316795 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570556 + SAMN41776210 + GSM8316795 + + 20042x1, WT PFC, Social 35, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570556 + SAMN41776210 + GSM8316795 + + + + + + + SRR29344850 + GSM8316795_r1 + + + + GSM8316795_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570556 + SAMN41776210 + GSM8316795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860523 + GSM8316794_r1 + + GSM8316794: 19957x3, WT PFC, Not, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570555 + GSM8316794 + + + + GSM8316794 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570555 + SAMN41776211 + GSM8316794 + + 19957x3, WT PFC, Not, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570555 + SAMN41776211 + GSM8316794 + + + + + + + SRR29344851 + GSM8316794_r1 + + + + GSM8316794_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570555 + SAMN41776211 + GSM8316794 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860522 + GSM8316793_r1 + + GSM8316793: 20523x1, WT PFC, Not, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570554 + GSM8316793 + + + + GSM8316793 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570554 + SAMN41776212 + GSM8316793 + + 20523x1, WT PFC, Not, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570554 + SAMN41776212 + GSM8316793 + + + + + + + SRR29344852 + GSM8316793_r1 + + + + GSM8316793_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570554 + SAMN41776212 + GSM8316793 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860521 + GSM8316792_r1 + + GSM8316792: 20521x1, WT PFC, Social 35, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570553 + GSM8316792 + + + + GSM8316792 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570553 + SAMN41776213 + GSM8316792 + + 20521x1, WT PFC, Social 35, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570553 + SAMN41776213 + GSM8316792 + + + + + + + SRR29344853 + GSM8316792_r1 + + + + GSM8316792_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570553 + SAMN41776213 + GSM8316792 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860520 + GSM8316791_r1 + + GSM8316791: 20375x6, WT PFC, Not, F; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570552 + GSM8316791 + + + + GSM8316791 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570552 + SAMN41776214 + GSM8316791 + + 20375x6, WT PFC, Not, F + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Not + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570552 + SAMN41776214 + GSM8316791 + + + + + + + SRR29344854 + GSM8316791_r1 + + + + GSM8316791_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570552 + SAMN41776214 + GSM8316791 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX24860519 + GSM8316790_r1 + + GSM8316790: 20251x1, WT PFC, Social 35, M; Mus musculus; RNA-Seq + + + SRP512939 + PRJNA1122152 + + + + + + + SRS21570551 + GSM8316790 + + + + GSM8316790 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor. Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA1894102 + SUB14520918 + + + + Frost Lab, Neurology, University of Utah + +
+ 383 Colorow Dr. + Salt Lake City + UT + USA +
+ + Nicholas + Frost + + + + + + SRP512939 + PRJNA1122152 + GSE269499 + + + Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction + + Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble Overall design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression. + GSE269499 + + + + + pubmed + 39045099 + + + + + pubmed + 39423127 + + + + + + + SRS21570551 + SAMN41776215 + GSM8316790 + + 20251x1, WT PFC, Social 35, M + + 10090 + Mus musculus + + + + + bioproject + 1122152 + + + + + + + source_name + Brain + + + tissue + Brain + + + region + medial prefrontal cortex + + + strain + c57bl6/J + + + treatment + Social 35 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21570551 + SAMN41776215 + GSM8316790 + + + + + + + SRR29344855 + GSM8316790_r1 + + + + GSM8316790_r1 + + + + + loader + fastq-load.py + + + + + + SRS21570551 + SAMN41776215 + GSM8316790 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE272062.xml b/tests/data/GSE272062.xml new file mode 100644 index 0000000..7e7d7a3 --- /dev/null +++ b/tests/data/GSE272062.xml @@ -0,0 +1,1216 @@ + + + + + + + SRX25286971 + GSM8392294_r1 + + GSM8392294: NeuN- cells from vehicle-treated brain, rep 3; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965721 + GSM8392294 + + + + GSM8392294 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965721 + SAMN42436319 + GSM8392294 + + NeuN- cells from vehicle-treated brain, rep 3 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + Vehicle + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965721 + SAMN42436319 + GSM8392294 + + + + + + + SRR29787081 + GSM8392294_r1 + + + + GSM8392294_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965721 + SAMN42436319 + GSM8392294 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX25286970 + GSM8392293_r1 + + GSM8392293: NeuN- cells from vehicle-treated brain, rep 2; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965720 + GSM8392293 + + + + GSM8392293 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965720 + SAMN42436320 + GSM8392293 + + NeuN- cells from vehicle-treated brain, rep 2 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + Vehicle + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965720 + SAMN42436320 + GSM8392293 + + + + + + + SRR29787082 + GSM8392293_r1 + + + + GSM8392293_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965720 + SAMN42436320 + GSM8392293 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25286969 + GSM8392292_r1 + + GSM8392292: NeuN- cells from vehicle-treated brain, rep 1; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965719 + GSM8392292 + + + + GSM8392292 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965719 + SAMN42436321 + GSM8392292 + + NeuN- cells from vehicle-treated brain, rep 1 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + Vehicle + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965719 + SAMN42436321 + GSM8392292 + + + + + + + SRR29787083 + GSM8392292_r1 + + + + GSM8392292_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965719 + SAMN42436321 + GSM8392292 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25286968 + GSM8392291_r1 + + GSM8392291: NeuN- cells from LPA-treated brain, rep 3; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965718 + GSM8392291 + + + + GSM8392291 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965718 + SAMN42436322 + GSM8392291 + + NeuN- cells from LPA-treated brain, rep 3 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + LPA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965718 + SAMN42436322 + GSM8392291 + + + + + + + SRR29787084 + GSM8392291_r1 + + + + GSM8392291_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965718 + SAMN42436322 + GSM8392291 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25286967 + GSM8392290_r1 + + GSM8392290: NeuN- cells from LPA-treated brain, rep 2; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965717 + GSM8392290 + + + + GSM8392290 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965717 + SAMN42436323 + GSM8392290 + + NeuN- cells from LPA-treated brain, rep 2 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + LPA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965717 + SAMN42436323 + GSM8392290 + + + + + + + SRR29787085 + GSM8392290_r1 + + + + GSM8392290_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965717 + SAMN42436323 + GSM8392290 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25286966 + GSM8392289_r1 + + GSM8392289: NeuN- cells from LPA-treated brain, rep 1; Mus musculus; RNA-Seq + + + SRP519373 + PRJNA1134761 + + + + + + + SRS21965716 + GSM8392289 + + + + GSM8392289 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice injected with LPA or vehicle were perfused with Hanks' Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei. Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells. + + + + + Illumina NovaSeq X + + + + + + SRA1922293 + SUB14598382 + + + + Sanford Burnham Prebys Medical Discovery Institute + +
+ 1090 N. Torrey Pines Rd + La Jolla + CA + USA +
+ + Jerold + Chun + + + + + + SRP519373 + PRJNA1134761 + GSE272062 + + + Lysophosphatidic acid (LPA)-dependent propagation of neuroinflammation in an optimized model of post-hemorrhagic hydrocephalus. + + Post-hemorrhagic hydrocephalus (PHH) is a neurological disease that primarily affects premature infants and involves infiltration of blood into the brain's ventricles followed by excessive accumulation of cerebrospinal fluid (CSF) leading to ventricular enlargement and increased intracranial pressure. However, the precise mechanisms driving PHH development and persistence remain incompletely known and lack medical and disease modifying treatments. Here we use a mouse model of PHH to identify transcriptomic, proteomic and cellular changes involving neurovascular and neuroimmunological microglial alterations as features of PHH, overlapping with those reported in human disease. Improvements on a lysophosphatidic acid (LPA)-initiated PHH mouse model were developed and combined with unbiased proteomic and single-nucleus transcriptomics that identified microglial molecular pathways promoting PHH. Pharmacological disruption of microglia in vivo significantly reduced PHH-associated ventriculomegaly. These data identify microglia and neurovascular molecular elements in the development of PHH, implicating them as potentially tractable therapeutic targets towards developing new treatments for PHH. Overall design: NeuN- nuclei were isolated from whole brains from mice treated with vehicle or LPA injection. 10x Genomics Single Cell 3' v3 kit was then used to prepare samples targeting 10,000 profiled cells + GSE272062 + + + + + SRS21965716 + SAMN42436324 + GSM8392289 + + NeuN- cells from LPA-treated brain, rep 1 + + 10090 + Mus musculus + + + + + bioproject + 1134761 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + NeuN- cells + + + treatment + LPA + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21965716 + SAMN42436324 + GSM8392289 + + + + + + + SRR29787086 + GSM8392289_r1 + + + + GSM8392289_r1 + + + + + loader + fastq-load.py + + + + + + SRS21965716 + SAMN42436324 + GSM8392289 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE272344.xml b/tests/data/GSE272344.xml new file mode 100644 index 0000000..611c597 --- /dev/null +++ b/tests/data/GSE272344.xml @@ -0,0 +1,1876 @@ + + + + + + + SRX25344180 + GSM8398841_r1 + + GSM8398841: Hippocampus, Li deficient, rep 5; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011389 + GSM8398841 + + + + GSM8398841 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011389 + SAMN42533718 + GSM8398841 + + Hippocampus, Li deficient, rep 5 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Li deficient diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011389 + SAMN42533718 + GSM8398841 + + + + + + + SRR29846342 + GSM8398841_r1 + + + + GSM8398841_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011389 + SAMN42533718 + GSM8398841 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344179 + GSM8398840_r1 + + GSM8398840: Hippocampus, Li deficient, rep 4; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011388 + GSM8398840 + + + + GSM8398840 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011388 + SAMN42533719 + GSM8398840 + + Hippocampus, Li deficient, rep 4 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Li deficient diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011388 + SAMN42533719 + GSM8398840 + + + + + + + SRR29846343 + GSM8398840_r1 + + + + GSM8398840_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011388 + SAMN42533719 + GSM8398840 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344178 + GSM8398839_r1 + + GSM8398839: Hippocampus, Li deficient, rep 3; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011387 + GSM8398839 + + + + GSM8398839 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011387 + SAMN42533720 + GSM8398839 + + Hippocampus, Li deficient, rep 3 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Li deficient diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011387 + SAMN42533720 + GSM8398839 + + + + + + + SRR29846344 + GSM8398839_r1 + + + + GSM8398839_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011387 + SAMN42533720 + GSM8398839 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344177 + GSM8398838_r1 + + GSM8398838: Hippocampus, Li deficient, rep 2; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011385 + GSM8398838 + + + + GSM8398838 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011385 + SAMN42533721 + GSM8398838 + + Hippocampus, Li deficient, rep 2 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Li deficient diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011385 + SAMN42533721 + GSM8398838 + + + + + + + SRR29846345 + GSM8398838_r1 + + + + GSM8398838_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011385 + SAMN42533721 + GSM8398838 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344176 + GSM8398837_r1 + + GSM8398837: Hippocampus, Li deficient, rep 1; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011386 + GSM8398837 + + + + GSM8398837 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011386 + SAMN42533722 + GSM8398837 + + Hippocampus, Li deficient, rep 1 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Li deficient diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011386 + SAMN42533722 + GSM8398837 + + + + + + + SRR29846346 + GSM8398837_r1 + + + + GSM8398837_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011386 + SAMN42533722 + GSM8398837 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344175 + GSM8398836_r1 + + GSM8398836: Hippocampus, Control, rep 4; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011384 + GSM8398836 + + + + GSM8398836 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011384 + SAMN42533723 + GSM8398836 + + Hippocampus, Control, rep 4 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Control diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011384 + SAMN42533723 + GSM8398836 + + + + + + + SRR29846347 + GSM8398836_r1 + + + + GSM8398836_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011384 + SAMN42533723 + GSM8398836 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344174 + GSM8398835_r1 + + GSM8398835: Hippocampus, Control, rep 3; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011381 + GSM8398835 + + + + GSM8398835 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011381 + SAMN42533724 + GSM8398835 + + Hippocampus, Control, rep 3 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Control diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011381 + SAMN42533724 + GSM8398835 + + + + + + + SRR29846348 + GSM8398835_r1 + + + + GSM8398835_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011381 + SAMN42533724 + GSM8398835 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344173 + GSM8398834_r1 + + GSM8398834: Hippocampus, Control, rep 2; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011382 + GSM8398834 + + + + GSM8398834 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011382 + SAMN42533725 + GSM8398834 + + Hippocampus, Control, rep 2 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Control diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011382 + SAMN42533725 + GSM8398834 + + + + + + + SRR29846349 + GSM8398834_r1 + + + + GSM8398834_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011382 + SAMN42533725 + GSM8398834 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25344172 + GSM8398833_r1 + + GSM8398833: Hippocampus, Control, rep 1; Mus musculus; RNA-Seq + + + SRP520250 + PRJNA1136488 + + + + + + + SRS22011383 + GSM8398833 + + + + GSM8398833 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were cardiac perfused with ice cold PBS and a cocktail of transcription inhibitors at a speed of 6mL/min for 8 mins to repress transcriptional response during the brain dissection and sample preparation. Hippocampal tissue was dissected on ice and flash frozen in liquid nitrogen. Both frozen hippocampal tissues were subsequently thawed together in 500µL of HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH=7.8, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) and homogenized with tight pestle of dounce homogenizer in the same HB buffer with additional 0.32% of IGEPAL (Sigma) (average of 25-30 times per sample) on ice. Subsequently, single nuclei were diluted to 9 mL in HB buffer, passed through the 40-μm filter and separated from debris and multinuclei by iodixanol gradient centrifugation. Specifically, we prepared 1 mL of 40% iodixanol in the bottom, 1 mL of 30% iodixanol in the middle layer and gently layered 9 mL of the diluted nuclei suspension on top of the 30% iodixanol layer for 18 minutes, 10,000g centrifugation. Single nuclei were recovered from the 30% iodixanol layer in between the 30% and 40% interface. An aliquot was taken for nuclei counting and visual inspection of nucleic morphology under the microscope. The rest of nucleic suspension was diluted for nuclei encapsulation and sequencing library preparation. The scRNA-seq libraries are prepared at the Harvard Single Cell Core, according to the 10X Genomics manual. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1925976 + SUB14607704 + + + + Harvard Medical School + +
+ 240 Longwood Ave + Boston + MA + USA +
+ + Danesh + Moazed + + + + + + SRP520250 + PRJNA1136488 + GSE272344 + + + Lithium Deficiency and the Onset of Alzheimer's Disease + + The non-genetic causes of Alzheimer's disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain. Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function. In addition, lithium is sequestered by aggregated amyloid ß-protein (Aß) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet. Loss of only 50% of endogenous brain Li resulted in markedly elevated Aß deposition through a predominant effect on Aß42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures. Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aß degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss. Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aß42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss. A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3ß. At the systems level, Li deficiency induced a state of neural hyperexcitation. To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate. LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain. Overall design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet. + GSE272344 + + + + + SRS22011383 + SAMN42533726 + GSM8398833 + + Hippocampus, Control, rep 1 + + 10090 + Mus musculus + + + + + bioproject + 1136488 + + + + + + + source_name + Mouse hippocampus + + + tissue + Mouse hippocampus + + + genotype + 3xTg + + + treatment + Control diet, 1 month + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22011383 + SAMN42533726 + GSM8398833 + + + + + + + SRR29846350 + GSM8398833_r1 + + + + GSM8398833_r1 + + + + + loader + fastq-load.py + + + + + + SRS22011383 + SAMN42533726 + GSM8398833 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE274763.xml b/tests/data/GSE274763.xml new file mode 100644 index 0000000..39d18e6 --- /dev/null +++ b/tests/data/GSE274763.xml @@ -0,0 +1,3136 @@ + + + + + + + SRX25689954 + GSM8457554_r1 + + GSM8457554: As3mtd2d3_tg, P60, replicate4, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332068 + GSM8457554 + + + + GSM8457554 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332068 + SAMN43168311 + GSM8457554 + + As3mtd2d3_tg, P60, replicate4, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332068 + SAMN43168311 + GSM8457554 + + + + + + + SRR30227725 + GSM8457554_r1 + + + + GSM8457554_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332068 + SAMN43168311 + GSM8457554 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227726 + GSM8457554_r2 + + + + GSM8457554_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332068 + SAMN43168311 + GSM8457554 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689953 + GSM8457553_r1 + + GSM8457553: As3mtd2d3_tg, P60, replicate3, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332067 + GSM8457553 + + + + GSM8457553 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332067 + SAMN43168312 + GSM8457553 + + As3mtd2d3_tg, P60, replicate3, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332067 + SAMN43168312 + GSM8457553 + + + + + + + SRR30227727 + GSM8457553_r1 + + + + GSM8457553_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332067 + SAMN43168312 + GSM8457553 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227728 + GSM8457553_r2 + + + + GSM8457553_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332067 + SAMN43168312 + GSM8457553 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689952 + GSM8457552_r1 + + GSM8457552: As3mtd2d3_tg, P60, replicate2, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332066 + GSM8457552 + + + + GSM8457552 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332066 + SAMN43168313 + GSM8457552 + + As3mtd2d3_tg, P60, replicate2, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332066 + SAMN43168313 + GSM8457552 + + + + + + + SRR30227729 + GSM8457552_r1 + + + + GSM8457552_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332066 + SAMN43168313 + GSM8457552 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227730 + GSM8457552_r2 + + + + GSM8457552_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332066 + SAMN43168313 + GSM8457552 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689951 + GSM8457551_r1 + + GSM8457551: As3mtd2d3_tg, P60, replicate1, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332065 + GSM8457551 + + + + GSM8457551 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332065 + SAMN43168314 + GSM8457551 + + As3mtd2d3_tg, P60, replicate1, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332065 + SAMN43168314 + GSM8457551 + + + + + + + SRR30227731 + GSM8457551_r1 + + + + GSM8457551_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332065 + SAMN43168314 + GSM8457551 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227732 + GSM8457551_r2 + + + + GSM8457551_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332065 + SAMN43168314 + GSM8457551 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689950 + GSM8457550_r1 + + GSM8457550: Control, P60, replicate4, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332064 + GSM8457550 + + + + GSM8457550 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332064 + SAMN43168315 + GSM8457550 + + Control, P60, replicate4, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332064 + SAMN43168315 + GSM8457550 + + + + + + + SRR30227733 + GSM8457550_r1 + + + + GSM8457550_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332064 + SAMN43168315 + GSM8457550 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227734 + GSM8457550_r2 + + + + GSM8457550_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332064 + SAMN43168315 + GSM8457550 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689949 + GSM8457549_r1 + + GSM8457549: Control, P60, replicate3, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332063 + GSM8457549 + + + + GSM8457549 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332063 + SAMN43168316 + GSM8457549 + + Control, P60, replicate3, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332063 + SAMN43168316 + GSM8457549 + + + + + + + SRR30227735 + GSM8457549_r1 + + + + GSM8457549_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332063 + SAMN43168316 + GSM8457549 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227736 + GSM8457549_r2 + + + + GSM8457549_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332063 + SAMN43168316 + GSM8457549 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689948 + GSM8457548_r1 + + GSM8457548: Control, P60, replicate2, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332062 + GSM8457548 + + + + GSM8457548 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332062 + SAMN43168317 + GSM8457548 + + Control, P60, replicate2, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332062 + SAMN43168317 + GSM8457548 + + + + + + + SRR30227737 + GSM8457548_r1 + + + + GSM8457548_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332062 + SAMN43168317 + GSM8457548 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227738 + GSM8457548_r2 + + + + GSM8457548_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332062 + SAMN43168317 + GSM8457548 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689947 + GSM8457547_r1 + + GSM8457547: Control, P60, replicate1, snRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332061 + GSM8457547 + + + + GSM8457547 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332061 + SAMN43168318 + GSM8457547 + + Control, P60, replicate1, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Postnatal day 60 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332061 + SAMN43168318 + GSM8457547 + + + + + + + SRR30227739 + GSM8457547_r1 + + + + GSM8457547_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332061 + SAMN43168318 + GSM8457547 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30227740 + GSM8457547_r2 + + + + GSM8457547_r1 + + + + + loader + fastq-load.py + + + + + + SRS22332061 + SAMN43168318 + GSM8457547 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689946 + GSM8457546_r1 + + GSM8457546: As3mtd2d3_tg, E15.5, replicate2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332060 + GSM8457546 + + + + GSM8457546 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332060 + SAMN43168319 + GSM8457546 + + As3mtd2d3_tg, E15.5, replicate2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Embryonic day 15.5 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332060 + SAMN43168319 + GSM8457546 + + + + + + + SRR30227741 + GSM8457546_r1 + + + + GSM8457546_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=E15.5_As3mtd2d3_tg_rep2_S1_L008_R1_001.fastq.gz --read2PairFiles=E15.5_As3mtd2d3_tg_rep2_S1_L008_R2_001.fastq.gz --read3PairFiles=E15.5_As3mtd2d3_tg_rep2_S1_L008_I1_001.fastq.gz --read4PairFiles=E15.5_As3mtd2d3_tg_rep2_S1_L008_I2_001.fastq.gz + + + + + + SRS22332060 + SAMN43168319 + GSM8457546 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689945 + GSM8457545_r1 + + GSM8457545: As3mtd2d3_tg, E15.5, replicate1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332059 + GSM8457545 + + + + GSM8457545 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332059 + SAMN43168320 + GSM8457545 + + As3mtd2d3_tg, E15.5, replicate1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre+) + + + age + Embryonic day 15.5 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332059 + SAMN43168320 + GSM8457545 + + + + + + + SRR30227742 + GSM8457545_r1 + + + + GSM8457545_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=E15.5_As3mtd2d3_tg_rep1_S1_L002_R1_001.fastq.gz --read2PairFiles=E15.5_As3mtd2d3_tg_rep1_S1_L002_R2_001.fastq.gz --read3PairFiles=E15.5_As3mtd2d3_tg_rep1_S1_L002_I1_001.fastq.gz --read4PairFiles=E15.5_As3mtd2d3_tg_rep1_S1_L002_I2_001.fastq.gz + + + + + + SRS22332059 + SAMN43168320 + GSM8457545 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689944 + GSM8457544_r1 + + GSM8457544: Control, E15.5, replicate2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332058 + GSM8457544 + + + + GSM8457544 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332058 + SAMN43168321 + GSM8457544 + + Control, E15.5, replicate2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Embryonic day 15.5 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332058 + SAMN43168321 + GSM8457544 + + + + + + + SRR30227743 + GSM8457544_r1 + + + + GSM8457544_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=E15.5_WT_rep2_S1_L007_R1_001.fastq.gz --read2PairFiles=E15.5_WT_rep2_S1_L007_R2_001.fastq.gz --read3PairFiles=E15.5_WT_rep2_S1_L007_I1_001.fastq.gz --read4PairFiles=E15.5_WT_rep2_S1_L007_I2_001.fastq.gz + + + + + + SRS22332058 + SAMN43168321 + GSM8457544 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25689943 + GSM8457543_r1 + + GSM8457543: Control, E15.5, replicate1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP526177 + GSE274763 + + + + + + + SRS22332057 + GSM8457543 + + + + GSM8457543 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100. For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1947059 + SUB14663578 + + + + Life science, Pohang University of Science and Technology(POSTECH) + +
+ 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673 + Pohang-si + South Korea +
+ + Dahun + Um + + + + + + SRP526177 + PRJNA1147777 + GSE274763 + + + Gene expression profile at single cell level of isofortex from Control and AS3MTd2d3-Tg mice + + Cell-type specific changes of isocortex in schizophrenia patients play critical roles in perception, cognition, emotion, and learning. We used single cell RNA sequencing(scRNA-seq) to analyze cell-type specific changes in AS3MTd2d3-Tg mice as a schizophrenia model. Overall design: To analyze using scRNAseq with E15.5, isocortex of AS3MT-Tg mice are dissected, digested with trypsin, and pipetted with Pasteur pipette to dissociate cells. To analyze using snRNAseq with P60, isocortex of AS3MT-Tg mice are applied to singulator to extract nuclei from cells. + GSE274763 + + + + + pubmed + 40153497 + + + + + + + SRS22332057 + SAMN43168322 + GSM8457543 + + Control, E15.5, replicate1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1147777 + + + + + + + source_name + Isocortex + + + tissue + Isocortex + + + strain + C57BL/6 + + + genotype + (AS3MTd2d3;Emx1-Cre-) + + + age + Embryonic day 15.5 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22332057 + SAMN43168322 + GSM8457543 + + + + + + + SRR30227744 + GSM8457543_r1 + + + + GSM8457543_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBTT --read1PairFiles=E15.5_WT_rep1_S3_L001_R1_001.fastq.gz --read2PairFiles=E15.5_WT_rep1_S3_L001_R2_001.fastq.gz --read3PairFiles=E15.5_WT_rep1_S3_L001_I1_001.fastq.gz --read4PairFiles=E15.5_WT_rep1_S3_L001_I2_001.fastq.gz + + + + + + SRS22332057 + SAMN43168322 + GSM8457543 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE274829.xml b/tests/data/GSE274829.xml new file mode 100644 index 0000000..80986db --- /dev/null +++ b/tests/data/GSE274829.xml @@ -0,0 +1,1871 @@ + + + + + + + SRX25707473 + GSM8458663_r1 + + GSM8458663: MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep2; Homo sapiens; RNA-Seq + + + SRP526470 + GSE274829 + + + + + + + SRS22348569 + GSM8458663 + + + + GSM8458663 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced. Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1948196 + SUB14666401 + + + + University of California, San Francisco + +
+ 400 Parnassus Ave + San Francisco + CA + USA +
+ + Laine + Goudy + + + + + + SRP526470 + PRJNA1148140 + GSE274829 + + + Microglia-derived IGF1 promotes neurogenesis of GABaergic neurons in perinatal human brain [MGEorganoid_scRNAseq] + + We conducted scRNAseq to investigate the transcriptomics of induced microglia (iMG) and iMG containing MGE-oriented organoids. Overall design: Human embryonic stem cells-induced microglia (iMG) were transplanted to 4-week-old MGE organoids. We conducted scRNAseq to investigate the transcriptomics of 6-week-old MGE organoids with and without iMG. We also used Fluorescence-activated cell sorting (FACS) to enrich GFP-labelled iMG and condcuted scRNAseq. + GSE274829 + + + + + SRS22348569 + SAMN43194512 + GSM8458663 + + MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep2 + + 9606 + Homo sapiens + + + + + bioproject + 1148140 + + + + + + + source_name + human organoids + + + tissue + human organoids + + + cell type + MGEo organoids + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22348569 + SAMN43194512 + GSM8458663 + + + + + + + SRR30245969 + GSM8458663_r1 + + + + GSM8458663_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348569 + SAMN43194512 + GSM8458663 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245970 + GSM8458663_r2 + + + + GSM8458663_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348569 + SAMN43194512 + GSM8458663 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25707472 + GSM8458661_r1 + + GSM8458661: MGEO,-iMG, 6wks organoids,rep2; Homo sapiens; RNA-Seq + + + SRP526470 + GSE274829 + + + + + + + SRS22348568 + GSM8458661 + + + + GSM8458661 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced. Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1948196 + SUB14666401 + + + + University of California, San Francisco + +
+ 400 Parnassus Ave + San Francisco + CA + USA +
+ + Laine + Goudy + + + + + + SRP526470 + PRJNA1148140 + GSE274829 + + + Microglia-derived IGF1 promotes neurogenesis of GABaergic neurons in perinatal human brain [MGEorganoid_scRNAseq] + + We conducted scRNAseq to investigate the transcriptomics of induced microglia (iMG) and iMG containing MGE-oriented organoids. Overall design: Human embryonic stem cells-induced microglia (iMG) were transplanted to 4-week-old MGE organoids. We conducted scRNAseq to investigate the transcriptomics of 6-week-old MGE organoids with and without iMG. We also used Fluorescence-activated cell sorting (FACS) to enrich GFP-labelled iMG and condcuted scRNAseq. + GSE274829 + + + + + SRS22348568 + SAMN43194514 + GSM8458661 + + MGEO,-iMG, 6wks organoids,rep2 + + 9606 + Homo sapiens + + + + + bioproject + 1148140 + + + + + + + source_name + human organoids + + + tissue + human organoids + + + cell type + MGEo organoids + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22348568 + SAMN43194514 + GSM8458661 + + + + + + + SRR30245971 + GSM8458661_r1 + + + + GSM8458661_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348568 + SAMN43194514 + GSM8458661 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245972 + GSM8458661_r2 + + + + GSM8458661_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348568 + SAMN43194514 + GSM8458661 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25707471 + GSM8458662_r1 + + GSM8458662: MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep1; Homo sapiens; RNA-Seq + + + SRP526470 + GSE274829 + + + + + + + SRS22348567 + GSM8458662 + + + + GSM8458662 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced. Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1948196 + SUB14666401 + + + + University of California, San Francisco + +
+ 400 Parnassus Ave + San Francisco + CA + USA +
+ + Laine + Goudy + + + + + + SRP526470 + PRJNA1148140 + GSE274829 + + + Microglia-derived IGF1 promotes neurogenesis of GABaergic neurons in perinatal human brain [MGEorganoid_scRNAseq] + + We conducted scRNAseq to investigate the transcriptomics of induced microglia (iMG) and iMG containing MGE-oriented organoids. Overall design: Human embryonic stem cells-induced microglia (iMG) were transplanted to 4-week-old MGE organoids. We conducted scRNAseq to investigate the transcriptomics of 6-week-old MGE organoids with and without iMG. We also used Fluorescence-activated cell sorting (FACS) to enrich GFP-labelled iMG and condcuted scRNAseq. + GSE274829 + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + MGEO,+iMG, 6wks organoids, 2wks post iMG transplantation, rep1 + + 9606 + Homo sapiens + + + + + bioproject + 1148140 + + + + + + + source_name + human organoids + + + tissue + human organoids + + + cell type + MGEo organoids + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + + + + + + SRR30245973 + GSM8458662_r1 + + + + GSM8458662_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245974 + GSM8458662_r2 + + + + GSM8458662_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245975 + GSM8458662_r3 + + + + GSM8458662_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245976 + GSM8458662_r4 + + + + GSM8458662_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348567 + SAMN43194513 + GSM8458662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25707470 + GSM8458660_r1 + + GSM8458660: MGEO,-iMG, 6wks organoids,rep1; Homo sapiens; RNA-Seq + + + SRP526470 + GSE274829 + + + + + + + SRS22348566 + GSM8458660 + + + + GSM8458660 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced. Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1948196 + SUB14666401 + + + + University of California, San Francisco + +
+ 400 Parnassus Ave + San Francisco + CA + USA +
+ + Laine + Goudy + + + + + + SRP526470 + PRJNA1148140 + GSE274829 + + + Microglia-derived IGF1 promotes neurogenesis of GABaergic neurons in perinatal human brain [MGEorganoid_scRNAseq] + + We conducted scRNAseq to investigate the transcriptomics of induced microglia (iMG) and iMG containing MGE-oriented organoids. Overall design: Human embryonic stem cells-induced microglia (iMG) were transplanted to 4-week-old MGE organoids. We conducted scRNAseq to investigate the transcriptomics of 6-week-old MGE organoids with and without iMG. We also used Fluorescence-activated cell sorting (FACS) to enrich GFP-labelled iMG and condcuted scRNAseq. + GSE274829 + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + MGEO,-iMG, 6wks organoids,rep1 + + 9606 + Homo sapiens + + + + + bioproject + 1148140 + + + + + + + source_name + human organoids + + + tissue + human organoids + + + cell type + MGEo organoids + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + + + + + + SRR30245977 + GSM8458660_r1 + + + + GSM8458660_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245978 + GSM8458660_r2 + + + + GSM8458660_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245979 + GSM8458660_r3 + + + + GSM8458660_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245980 + GSM8458660_r4 + + + + GSM8458660_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348566 + SAMN43194515 + GSM8458660 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25707469 + GSM8458659_r1 + + GSM8458659: iMG, GFP-enriched, 6wk organoid, 2wk post iMG transplantation; Homo sapiens; RNA-Seq + + + SRP526470 + GSE274829 + + + + + + + SRS22348565 + GSM8458659 + + + + GSM8458659 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + MGE organoids were enzymatically digested, filtered, and resuspend for scRNAseq. GFP-labelled iMG were sorted by FACS and then sequenced. Library was performed accoding to manufacter's instructions (single cell v3.1), targeting 5,000 cells/nuclei per library. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1948196 + SUB14666401 + + + + University of California, San Francisco + +
+ 400 Parnassus Ave + San Francisco + CA + USA +
+ + Laine + Goudy + + + + + + SRP526470 + PRJNA1148140 + GSE274829 + + + Microglia-derived IGF1 promotes neurogenesis of GABaergic neurons in perinatal human brain [MGEorganoid_scRNAseq] + + We conducted scRNAseq to investigate the transcriptomics of induced microglia (iMG) and iMG containing MGE-oriented organoids. Overall design: Human embryonic stem cells-induced microglia (iMG) were transplanted to 4-week-old MGE organoids. We conducted scRNAseq to investigate the transcriptomics of 6-week-old MGE organoids with and without iMG. We also used Fluorescence-activated cell sorting (FACS) to enrich GFP-labelled iMG and condcuted scRNAseq. + GSE274829 + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + iMG, GFP-enriched, 6wk organoid, 2wk post iMG transplantation + + 9606 + Homo sapiens + + + + + bioproject + 1148140 + + + + + + + source_name + human organoids + + + tissue + human organoids + + + cell type + induced microglia + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + + + + + + SRR30245981 + GSM8458659_r1 + + + + GSM8458659_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245982 + GSM8458659_r2 + + + + GSM8458659_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245983 + GSM8458659_r3 + + + + GSM8458659_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30245984 + GSM8458659_r4 + + + + GSM8458659_r1 + + + + + loader + fastq-load.py + + + + + + SRS22348565 + SAMN43194516 + GSM8458659 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE275205.xml b/tests/data/GSE275205.xml new file mode 100644 index 0000000..f8c6d39 --- /dev/null +++ b/tests/data/GSE275205.xml @@ -0,0 +1,1700 @@ + + + + + + + SRX25758979 + GSM8472699_r1 + + GSM8472699: Cohort 2-RSD-PLX; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398115 + GSM8472699 + + + + GSM8472699 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398115 + SAMN43259621 + GSM8472699 + + Cohort 2-RSD-PLX + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + PLX Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398115 + SAMN43259621 + GSM8472699 + + + + + + + SRR30298488 + GSM8472699_r1 + + + + GSM8472699_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=PLXRSD_CKDL200160959-1a-SI_GA_E4_HCJJKBBXX_S1_L002_I1_001.fastq.gz --read2PairFiles=PLXRSD_CKDL200160959-1a-SI_GA_E4_HCJJKBBXX_S1_L002_R1_001.fastq.gz --read3PairFiles=PLXRSD_CKDL200160959-1a-SI_GA_E4_HCJJKBBXX_S1_L002_R2_001.fastq.gz + + + + + + SRS22398115 + SAMN43259621 + GSM8472699 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758978 + GSM8472698_r1 + + GSM8472698: Cohort 2-Control-PLX; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398117 + GSM8472698 + + + + GSM8472698 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398117 + SAMN43259622 + GSM8472698 + + Cohort 2-Control-PLX + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + PLX Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398117 + SAMN43259622 + GSM8472698 + + + + + + + SRR30298489 + GSM8472698_r1 + + + + GSM8472698_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=PLXCon_CKDL200160957-1a-SI_GA_E2_HCJJKBBXX_S2_L002_I1_001.fastq.gz --read2PairFiles=PLXCon_CKDL200160957-1a-SI_GA_E2_HCJJKBBXX_S2_L002_R1_001.fastq.gz --read3PairFiles=PLXCon_CKDL200160957-1a-SI_GA_E2_HCJJKBBXX_S2_L002_R2_001.fastq.gz + + + + + + SRS22398117 + SAMN43259622 + GSM8472698 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758977 + GSM8472697_r1 + + GSM8472697: Cohort 2-RSD-Veh; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398116 + GSM8472697 + + + + GSM8472697 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398116 + SAMN43259623 + GSM8472697 + + Cohort 2-RSD-Veh + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + Control Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398116 + SAMN43259623 + GSM8472697 + + + + + + + SRR30298490 + GSM8472697_r1 + + + + GSM8472697_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=VehRSD_CKDL200160958-1a-SI_GA_E3_HCJJKBBXX_S3_L002_I1_001.fastq.gz --read2PairFiles=VehRSD_CKDL200160958-1a-SI_GA_E3_HCJJKBBXX_S3_L002_R1_001.fastq.gz --read3PairFiles=VehRSD_CKDL200160958-1a-SI_GA_E3_HCJJKBBXX_S3_L002_R2_001.fastq.gz + + + + + + SRS22398116 + SAMN43259623 + GSM8472697 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758976 + GSM8472696_r1 + + GSM8472696: Cohort 2-Control-Veh; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398119 + GSM8472696 + + + + GSM8472696 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398119 + SAMN43259624 + GSM8472696 + + Cohort 2-Control-Veh + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + Control Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398119 + SAMN43259624 + GSM8472696 + + + + + + + SRR30298491 + GSM8472696_r1 + + + + GSM8472696_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=VehCon_CKDL200160956-1a-SI_GA_E1_HCJJKBBXX_S4_L002_I1_001.fastq.gz --read2PairFiles=VehCon_CKDL200160956-1a-SI_GA_E1_HCJJKBBXX_S4_L002_R1_001.fastq.gz --read3PairFiles=VehCon_CKDL200160956-1a-SI_GA_E1_HCJJKBBXX_S4_L002_R2_001.fastq.gz + + + + + + SRS22398119 + SAMN43259624 + GSM8472696 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758975 + GSM8472695_r1 + + GSM8472695: Cohort 1-RSD-PLX; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398118 + GSM8472695 + + + + GSM8472695 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398118 + SAMN43259625 + GSM8472695 + + Cohort 1-RSD-PLX + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + PLX Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398118 + SAMN43259625 + GSM8472695 + + + + + + + SRR30298492 + GSM8472695_r1 + + + + GSM8472695_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=PLXRSD_S4_L003_I1_001.fastq.gz --read2PairFiles=PLXRSD_S4_L003_R1_001.fastq.gz --read3PairFiles=PLXRSD_S4_L003_R2_001.fastq.gz + + + + + + SRS22398118 + SAMN43259625 + GSM8472695 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758974 + GSM8472694_r1 + + GSM8472694: Cohort 1-Control-PLX; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398114 + GSM8472694 + + + + GSM8472694 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398114 + SAMN43259626 + GSM8472694 + + Cohort 1-Control-PLX + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + PLX Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398114 + SAMN43259626 + GSM8472694 + + + + + + + SRR30298493 + GSM8472694_r1 + + + + GSM8472694_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=PLXCon_S3_L003_I1_001.fastq.gz --read2PairFiles=PLXCon_S3_L003_R1_001.fastq.gz --read3PairFiles=PLXCon_S3_L003_R2_001.fastq.gz + + + + + + SRS22398114 + SAMN43259626 + GSM8472694 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758973 + GSM8472693_r1 + + GSM8472693: Cohort 1-RSD-Veh; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398113 + GSM8472693 + + + + GSM8472693 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398113 + SAMN43259627 + GSM8472693 + + Cohort 1-RSD-Veh + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + Control Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398113 + SAMN43259627 + GSM8472693 + + + + + + + SRR30298494 + GSM8472693_r1 + + + + GSM8472693_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=VehRSD_S2_L003_I1_001.fastq.gz --read2PairFiles=VehRSD_S2_L003_R1_001.fastq.gz --read3PairFiles=VehRSD_S2_L003_R2_001.fastq.gz + + + + + + SRS22398113 + SAMN43259627 + GSM8472693 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX25758972 + GSM8472692_r1 + + GSM8472692: Cohort 1-Control-Veh; Mus musculus; RNA-Seq + + + SRP527371 + GSE275205 + + + + + + + SRS22398120 + GSM8472692 + + + + GSM8472692 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice mice underwent CO2 asphyxiation and were perfused with phosphate buffered saline (PBS). The hippocampus was dissected and dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit per manufacturer's instructions with minor modifications. Tissue was immediately placed into Enzyme P solution (37°C), Enzyme A solution was added, and tissue was dissociated in C-tubes using a gentleMACS dissociator. Density centrifugation was used to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Hippocampi from three mice per group were pooled into each sample. This experiment was performed in two replicates, with six mice per group total, and approximately 3,000-5,000 cells were recovered from each sample. Single-cell suspension was loaded onto a 10X chip and run on a Chromium Controller to generate gel-bead emulsions. Protocols for UMI barcoding, cDNA amplification, and library construction followed the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 kit protocol (10x Genomics; 1000121). Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip and was sequenced using an Illumina HiSeq. + + + + + Illumina HiSeq 4000 + + + + + + SRA1951096 + SUB14673744 + + + + Ohio State University + +
+ Gateway Lofts Columbus, 2211 Dublin Rd + COLUMBUS + OH + USA +
+ + Zhuoxin + Zhou + + + + + + SRP527371 + PRJNA1149800 + GSE275205 + + + Single Cell RNAseq of the hippocampus after RSD following microglia depletion + + Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits. Overall design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing + GSE275205 + + + + + pubmed + 39341879 + + + + + + + SRS22398120 + SAMN43259628 + GSM8472692 + + Cohort 1-Control-Veh + + 10090 + Mus musculus + + + + + bioproject + 1149800 + + + + + + + source_name + hippocampus + + + tissue + hippocampus + + + treatment + Control Diet + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22398120 + SAMN43259628 + GSM8472692 + + + + + + + SRR30298495 + GSM8472692_r1 + + + + GSM8472692_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TBB --read1PairFiles=VehCon_S1_L003_I1_001.fastq.gz --read2PairFiles=VehCon_S1_L003_R1_001.fastq.gz --read3PairFiles=VehCon_S1_L003_R2_001.fastq.gz + + + + + + SRS22398120 + SAMN43259628 + GSM8472692 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE279548.xml b/tests/data/GSE279548.xml new file mode 100644 index 0000000..bf32185 --- /dev/null +++ b/tests/data/GSE279548.xml @@ -0,0 +1,824 @@ + + + + + + + SRX26391770 + GSM8574964_r1 + + GSM8574964: in vivo Ago2 KO brain cells, replicate 2; Mus musculus; RNA-Seq + + + SRP538740 + GSE279548 + + + + + + + SRS22914737 + GSM8574964 + + + + GSM8574964 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Snap frozen hemispheres of mice at age P14 were minced on ice into 1 mm x 1 mm pieces, dounced in 2 ml ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2 U/ul recombinant RNase inhibitor (Takara)) and lysed on ice for 5 minutes. Lysis was stopped by adding 10 ml of ice-cold PBS-BSA (1% BSA, 0.2 U/ul RNase inhibitor), the suspension was filtered through a 40 mm cell strainer and centrifuged at 4°C, 500g for 5 minutes. Nuclei were washed two times with PBS-BSA, counted and assessed for quality. Immediately before loading nuclei on the 10x Chromium, nuclei were washed and concentrated to remove potential ambient RNA. Post wash between 2000 and 5000 nuclei were loaded onto the 10X Chromium System for nuclei encapsulation as per the manufacturer's instructions in Chromium Single Cell 3' Reagents kit v3 user guide RevC. Libraries were prepared using Single Cell 3' v3 chemistry. Briefly, RNA was reverse transcribed in the gel bead emulsion and cDNA amplified adding three additional PCR cycles to compensate for low RNA content of nuclei as compared to cells. Subsequently, libraries were fragmented and indexed. Final libraries were quantified and assessed for fragments size using the Agilent 4200 Tapestation System. Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1992149 + SUB14793654 + + + + Translational Nutrition Biology, Health Sciences and Technology, ETH Zurich + +
+ Schorenstrasse 16 + Schwerzenbach + Switzerland +
+ + Adhideb + Ghosh + + + + + + SRP538740 + PRJNA1173227 + GSE279548 + + + Glutamatergic argonaute2 promotes the formation of the neurovascular unit in mice + + Proper formation of the complex neurovascular unit (NVU) along with the blood-brain barrier is critical for building and sustaining a healthy, functioning central nervous system. The RNA binding protein argonaute2 (Ago2) mediates microRNA (miRNA)–mediated gene silencing, which is critical for many facets of brain development, including NVU development. Here, we found that Ago2 in glutamatergic neurons was critical for NVU formation in the developing cortices of mice. Glutamatergic neuron–specific loss of Ago2 diminished synaptic formation, neuronal-to-endothelial cell contacts, and morphogenesis of the brain vasculature, ultimately compromising the integrity of the blood-brain barrier. Ago2 facilitated miRNA targeting of phosphatase and tensin homolog (Pten) mRNA, which encodes a phosphatase that modulates reelin-dependent phosphatidylinositol 3-kinase (PI3K)–Akt signaling within the glutamatergic subpopulation. Conditionally deleting Pten in Ago2-deficient neurons restored Akt2 phosphorylation as well as postnatal development and survival. Several mutations in AGO2 impair small RNA silencing and are associated with Lessel-Kreienkamp syndrome, a neurodevelopmental disorder. When expressed in a neuronal cell line, these human AGO2 loss-of-function variants failed to suppress PTEN, resulting in attenuated PI3K-Akt signaling, further indicating that dysregulation of Ago2 function may contribute to both impaired development and neurological disorders. Together, these results identify Ago2 as central to the engagement of neurons with blood vessels in the developing brain. Overall design: To understand the role of endogenous Ago2 in the CNS, we generate a mutant mouse line where Ago2 expression was deleted in Vglut2-expressing excitatory neurons (by crossing the Slc17a6-Cre mouse line with an Ago2 conditional allele, Slc17a6-Cre, Ago2flox/flox mice). The cortical cells will be isolated from mice brain at P14 for scRNAseq analysis + GSE279548 + + + + + pubmed + 39999211 + + + + + + + SRS22914737 + SAMN44296831 + GSM8574964 + + in vivo Ago2 KO brain cells, replicate 2 + + 10090 + Mus musculus + + + + + bioproject + 1173227 + + + + + + + source_name + brain + + + cell type + brain cells + + + tissue + brain + + + strain + C57BL/6 + + + genotype + Slc17a6-Cre, Ago2 flox/flox + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22914737 + SAMN44296831 + GSM8574964 + + + + + + + SRR31004273 + GSM8574964_r1 + + + + GSM8574964_r1 + + + + + + SRS22914737 + SAMN44296831 + GSM8574964 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26391769 + GSM8574963_r1 + + GSM8574963: in vivo Ago2 KO brain cells, replicate 1; Mus musculus; RNA-Seq + + + SRP538740 + GSE279548 + + + + + + + SRS22914736 + GSM8574963 + + + + GSM8574963 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Snap frozen hemispheres of mice at age P14 were minced on ice into 1 mm x 1 mm pieces, dounced in 2 ml ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2 U/ul recombinant RNase inhibitor (Takara)) and lysed on ice for 5 minutes. Lysis was stopped by adding 10 ml of ice-cold PBS-BSA (1% BSA, 0.2 U/ul RNase inhibitor), the suspension was filtered through a 40 mm cell strainer and centrifuged at 4°C, 500g for 5 minutes. Nuclei were washed two times with PBS-BSA, counted and assessed for quality. Immediately before loading nuclei on the 10x Chromium, nuclei were washed and concentrated to remove potential ambient RNA. Post wash between 2000 and 5000 nuclei were loaded onto the 10X Chromium System for nuclei encapsulation as per the manufacturer's instructions in Chromium Single Cell 3' Reagents kit v3 user guide RevC. Libraries were prepared using Single Cell 3' v3 chemistry. Briefly, RNA was reverse transcribed in the gel bead emulsion and cDNA amplified adding three additional PCR cycles to compensate for low RNA content of nuclei as compared to cells. Subsequently, libraries were fragmented and indexed. Final libraries were quantified and assessed for fragments size using the Agilent 4200 Tapestation System. Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1992149 + SUB14793654 + + + + Translational Nutrition Biology, Health Sciences and Technology, ETH Zurich + +
+ Schorenstrasse 16 + Schwerzenbach + Switzerland +
+ + Adhideb + Ghosh + + + + + + SRP538740 + PRJNA1173227 + GSE279548 + + + Glutamatergic argonaute2 promotes the formation of the neurovascular unit in mice + + Proper formation of the complex neurovascular unit (NVU) along with the blood-brain barrier is critical for building and sustaining a healthy, functioning central nervous system. The RNA binding protein argonaute2 (Ago2) mediates microRNA (miRNA)–mediated gene silencing, which is critical for many facets of brain development, including NVU development. Here, we found that Ago2 in glutamatergic neurons was critical for NVU formation in the developing cortices of mice. Glutamatergic neuron–specific loss of Ago2 diminished synaptic formation, neuronal-to-endothelial cell contacts, and morphogenesis of the brain vasculature, ultimately compromising the integrity of the blood-brain barrier. Ago2 facilitated miRNA targeting of phosphatase and tensin homolog (Pten) mRNA, which encodes a phosphatase that modulates reelin-dependent phosphatidylinositol 3-kinase (PI3K)–Akt signaling within the glutamatergic subpopulation. Conditionally deleting Pten in Ago2-deficient neurons restored Akt2 phosphorylation as well as postnatal development and survival. Several mutations in AGO2 impair small RNA silencing and are associated with Lessel-Kreienkamp syndrome, a neurodevelopmental disorder. When expressed in a neuronal cell line, these human AGO2 loss-of-function variants failed to suppress PTEN, resulting in attenuated PI3K-Akt signaling, further indicating that dysregulation of Ago2 function may contribute to both impaired development and neurological disorders. Together, these results identify Ago2 as central to the engagement of neurons with blood vessels in the developing brain. Overall design: To understand the role of endogenous Ago2 in the CNS, we generate a mutant mouse line where Ago2 expression was deleted in Vglut2-expressing excitatory neurons (by crossing the Slc17a6-Cre mouse line with an Ago2 conditional allele, Slc17a6-Cre, Ago2flox/flox mice). The cortical cells will be isolated from mice brain at P14 for scRNAseq analysis + GSE279548 + + + + + pubmed + 39999211 + + + + + + + SRS22914736 + SAMN44296832 + GSM8574963 + + in vivo Ago2 KO brain cells, replicate 1 + + 10090 + Mus musculus + + + + + bioproject + 1173227 + + + + + + + source_name + brain + + + cell type + brain cells + + + tissue + brain + + + strain + C57BL/6 + + + genotype + Slc17a6-Cre, Ago2 flox/flox + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22914736 + SAMN44296832 + GSM8574963 + + + + + + + SRR31004274 + GSM8574963_r1 + + + + GSM8574963_r1 + + + + + + SRS22914736 + SAMN44296832 + GSM8574963 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26391768 + GSM8574962_r1 + + GSM8574962: in vivo Ago2 WT brain cells, replicate 2; Mus musculus; RNA-Seq + + + SRP538740 + GSE279548 + + + + + + + SRS22914735 + GSM8574962 + + + + GSM8574962 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Snap frozen hemispheres of mice at age P14 were minced on ice into 1 mm x 1 mm pieces, dounced in 2 ml ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2 U/ul recombinant RNase inhibitor (Takara)) and lysed on ice for 5 minutes. Lysis was stopped by adding 10 ml of ice-cold PBS-BSA (1% BSA, 0.2 U/ul RNase inhibitor), the suspension was filtered through a 40 mm cell strainer and centrifuged at 4°C, 500g for 5 minutes. Nuclei were washed two times with PBS-BSA, counted and assessed for quality. Immediately before loading nuclei on the 10x Chromium, nuclei were washed and concentrated to remove potential ambient RNA. Post wash between 2000 and 5000 nuclei were loaded onto the 10X Chromium System for nuclei encapsulation as per the manufacturer's instructions in Chromium Single Cell 3' Reagents kit v3 user guide RevC. Libraries were prepared using Single Cell 3' v3 chemistry. Briefly, RNA was reverse transcribed in the gel bead emulsion and cDNA amplified adding three additional PCR cycles to compensate for low RNA content of nuclei as compared to cells. Subsequently, libraries were fragmented and indexed. Final libraries were quantified and assessed for fragments size using the Agilent 4200 Tapestation System. Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1992149 + SUB14793654 + + + + Translational Nutrition Biology, Health Sciences and Technology, ETH Zurich + +
+ Schorenstrasse 16 + Schwerzenbach + Switzerland +
+ + Adhideb + Ghosh + + + + + + SRP538740 + PRJNA1173227 + GSE279548 + + + Glutamatergic argonaute2 promotes the formation of the neurovascular unit in mice + + Proper formation of the complex neurovascular unit (NVU) along with the blood-brain barrier is critical for building and sustaining a healthy, functioning central nervous system. The RNA binding protein argonaute2 (Ago2) mediates microRNA (miRNA)–mediated gene silencing, which is critical for many facets of brain development, including NVU development. Here, we found that Ago2 in glutamatergic neurons was critical for NVU formation in the developing cortices of mice. Glutamatergic neuron–specific loss of Ago2 diminished synaptic formation, neuronal-to-endothelial cell contacts, and morphogenesis of the brain vasculature, ultimately compromising the integrity of the blood-brain barrier. Ago2 facilitated miRNA targeting of phosphatase and tensin homolog (Pten) mRNA, which encodes a phosphatase that modulates reelin-dependent phosphatidylinositol 3-kinase (PI3K)–Akt signaling within the glutamatergic subpopulation. Conditionally deleting Pten in Ago2-deficient neurons restored Akt2 phosphorylation as well as postnatal development and survival. Several mutations in AGO2 impair small RNA silencing and are associated with Lessel-Kreienkamp syndrome, a neurodevelopmental disorder. When expressed in a neuronal cell line, these human AGO2 loss-of-function variants failed to suppress PTEN, resulting in attenuated PI3K-Akt signaling, further indicating that dysregulation of Ago2 function may contribute to both impaired development and neurological disorders. Together, these results identify Ago2 as central to the engagement of neurons with blood vessels in the developing brain. Overall design: To understand the role of endogenous Ago2 in the CNS, we generate a mutant mouse line where Ago2 expression was deleted in Vglut2-expressing excitatory neurons (by crossing the Slc17a6-Cre mouse line with an Ago2 conditional allele, Slc17a6-Cre, Ago2flox/flox mice). The cortical cells will be isolated from mice brain at P14 for scRNAseq analysis + GSE279548 + + + + + pubmed + 39999211 + + + + + + + SRS22914735 + SAMN44296833 + GSM8574962 + + in vivo Ago2 WT brain cells, replicate 2 + + 10090 + Mus musculus + + + + + bioproject + 1173227 + + + + + + + source_name + brain + + + cell type + brain cells + + + tissue + brain + + + strain + C57BL/6 + + + genotype + Slc17a6-Cre, Ago2 wt/wt + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22914735 + SAMN44296833 + GSM8574962 + + + + + + + SRR31004275 + GSM8574962_r1 + + + + GSM8574962_r1 + + + + + + SRS22914735 + SAMN44296833 + GSM8574962 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26391767 + GSM8574961_r1 + + GSM8574961: in vivo Ago2 WT brain cells, replicate 1; Mus musculus; RNA-Seq + + + SRP538740 + GSE279548 + + + + + + + SRS22914734 + GSM8574961 + + + + GSM8574961 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Snap frozen hemispheres of mice at age P14 were minced on ice into 1 mm x 1 mm pieces, dounced in 2 ml ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2 U/ul recombinant RNase inhibitor (Takara)) and lysed on ice for 5 minutes. Lysis was stopped by adding 10 ml of ice-cold PBS-BSA (1% BSA, 0.2 U/ul RNase inhibitor), the suspension was filtered through a 40 mm cell strainer and centrifuged at 4°C, 500g for 5 minutes. Nuclei were washed two times with PBS-BSA, counted and assessed for quality. Immediately before loading nuclei on the 10x Chromium, nuclei were washed and concentrated to remove potential ambient RNA. Post wash between 2000 and 5000 nuclei were loaded onto the 10X Chromium System for nuclei encapsulation as per the manufacturer's instructions in Chromium Single Cell 3' Reagents kit v3 user guide RevC. Libraries were prepared using Single Cell 3' v3 chemistry. Briefly, RNA was reverse transcribed in the gel bead emulsion and cDNA amplified adding three additional PCR cycles to compensate for low RNA content of nuclei as compared to cells. Subsequently, libraries were fragmented and indexed. Final libraries were quantified and assessed for fragments size using the Agilent 4200 Tapestation System. Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina). + + + + + Illumina NovaSeq 6000 + + + + + + SRA1992149 + SUB14793654 + + + + Translational Nutrition Biology, Health Sciences and Technology, ETH Zurich + +
+ Schorenstrasse 16 + Schwerzenbach + Switzerland +
+ + Adhideb + Ghosh + + + + + + SRP538740 + PRJNA1173227 + GSE279548 + + + Glutamatergic argonaute2 promotes the formation of the neurovascular unit in mice + + Proper formation of the complex neurovascular unit (NVU) along with the blood-brain barrier is critical for building and sustaining a healthy, functioning central nervous system. The RNA binding protein argonaute2 (Ago2) mediates microRNA (miRNA)–mediated gene silencing, which is critical for many facets of brain development, including NVU development. Here, we found that Ago2 in glutamatergic neurons was critical for NVU formation in the developing cortices of mice. Glutamatergic neuron–specific loss of Ago2 diminished synaptic formation, neuronal-to-endothelial cell contacts, and morphogenesis of the brain vasculature, ultimately compromising the integrity of the blood-brain barrier. Ago2 facilitated miRNA targeting of phosphatase and tensin homolog (Pten) mRNA, which encodes a phosphatase that modulates reelin-dependent phosphatidylinositol 3-kinase (PI3K)–Akt signaling within the glutamatergic subpopulation. Conditionally deleting Pten in Ago2-deficient neurons restored Akt2 phosphorylation as well as postnatal development and survival. Several mutations in AGO2 impair small RNA silencing and are associated with Lessel-Kreienkamp syndrome, a neurodevelopmental disorder. When expressed in a neuronal cell line, these human AGO2 loss-of-function variants failed to suppress PTEN, resulting in attenuated PI3K-Akt signaling, further indicating that dysregulation of Ago2 function may contribute to both impaired development and neurological disorders. Together, these results identify Ago2 as central to the engagement of neurons with blood vessels in the developing brain. Overall design: To understand the role of endogenous Ago2 in the CNS, we generate a mutant mouse line where Ago2 expression was deleted in Vglut2-expressing excitatory neurons (by crossing the Slc17a6-Cre mouse line with an Ago2 conditional allele, Slc17a6-Cre, Ago2flox/flox mice). The cortical cells will be isolated from mice brain at P14 for scRNAseq analysis + GSE279548 + + + + + pubmed + 39999211 + + + + + + + SRS22914734 + SAMN44296834 + GSM8574961 + + in vivo Ago2 WT brain cells, replicate 1 + + 10090 + Mus musculus + + + + + bioproject + 1173227 + + + + + + + source_name + brain + + + cell type + brain cells + + + tissue + brain + + + strain + C57BL/6 + + + genotype + Slc17a6-Cre, Ago2 wt/wt + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22914734 + SAMN44296834 + GSM8574961 + + + + + + + SRR31004276 + GSM8574961_r1 + + + + GSM8574961_r1 + + + + + + SRS22914734 + SAMN44296834 + GSM8574961 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE280296.xml b/tests/data/GSE280296.xml new file mode 100644 index 0000000..20e1cd5 --- /dev/null +++ b/tests/data/GSE280296.xml @@ -0,0 +1,7650 @@ + + + + + + + SRX28385049 + GSM8907926_r1 + + GSM8907926: CUT&RUN_REP2; Mus musculus; OTHER + + + SRP540808 + PRJNA1177781 + + + + + + + SRS24708986 + GSM8907926 + + + + GSM8907926 + OTHER + GENOMIC + other + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111158 + SUB15256580 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS24708986 + SAMN47937638 + GSM8907926 + + CUT&RUN_REP2 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell line + Adult hippocampuse derived neural stem cell culture + + + cell type + adult hippocampal neural stem cells + + + genotype + wildtype + + + treatment + no treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24708986 + SAMN47937638 + GSM8907926 + + + + + + + SRR33121467 + GSM8907926_r1 + + + + GSM8907926_r1 + + + + + + SRS24708986 + SAMN47937638 + GSM8907926 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28385048 + GSM8907925_r1 + + GSM8907925: CUT&RUN_REP1; Mus musculus; OTHER + + + SRP540808 + PRJNA1177781 + + + + + + + SRS24708985 + GSM8907925 + + + + GSM8907925 + OTHER + GENOMIC + other + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111158 + SUB15256580 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS24708985 + SAMN47937639 + GSM8907925 + + CUT&RUN_REP1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell line + Adult hippocampuse derived neural stem cell culture + + + cell type + adult hippocampal neural stem cells + + + genotype + wildtype + + + treatment + no treatment + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24708985 + SAMN47937639 + GSM8907925 + + + + + + + SRR33121468 + GSM8907925_r1 + + + + GSM8907925_r1 + + + + + + SRS24708985 + SAMN47937639 + GSM8907925 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496514 + GSM8594269_r1 + + GSM8594269: Huwe1_control_rep2; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009433 + GSM8594269 + + + + GSM8594269 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009433 + SAMN44450840 + GSM8594269 + + Huwe1_control_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Huwe1_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009433 + SAMN44450840 + GSM8594269 + + + + + + + SRR31114271 + GSM8594269_r1 + + + + GSM8594269_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009433 + SAMN44450840 + GSM8594269 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496513 + GSM8594268_r1 + + GSM8594268: Huwe1_cKO_rep2; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009432 + GSM8594268 + + + + GSM8594268 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009432 + SAMN44450841 + GSM8594268 + + Huwe1_cKO_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Huwe1_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009432 + SAMN44450841 + GSM8594268 + + + + + + + SRR31114275 + GSM8594268_r1 + + + + GSM8594268_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009432 + SAMN44450841 + GSM8594268 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496512 + GSM8594267_r1 + + GSM8594267: Ascl1_control_rep3; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009431 + GSM8594267 + + + + GSM8594267 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + Ascl1_control_rep3 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + + + + + + SRR31114279 + GSM8594267_r1 + + + + GSM8594267_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114280 + GSM8594267_r2 + + + + GSM8594267_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114281 + GSM8594267_r3 + + + + GSM8594267_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114282 + GSM8594267_r4 + + + + GSM8594267_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009431 + SAMN44450842 + GSM8594267 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496511 + GSM8594266_r1 + + GSM8594266: Ascl1_cKO_rep3; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009429 + GSM8594266 + + + + GSM8594266 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009429 + SAMN44450843 + GSM8594266 + + Ascl1_cKO_rep3 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009429 + SAMN44450843 + GSM8594266 + + + + + + + SRR31114283 + GSM8594266_r1 + + + + GSM8594266_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009429 + SAMN44450843 + GSM8594266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR31114285 + GSM8594266_r3 + + + + GSM8594266_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009429 + SAMN44450843 + GSM8594266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114286 + GSM8594266_r4 + + + + GSM8594266_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009429 + SAMN44450843 + GSM8594266 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496510 + GSM8594265_r1 + + GSM8594265: Ascl1_sample2_rep2_demultiplex_required; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009430 + GSM8594265 + + + + GSM8594265 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009430 + SAMN44450844 + GSM8594265 + + Ascl1_sample2_rep2_demultiplex_required + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_sample2_rep2_demultiplex_required + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009430 + SAMN44450844 + GSM8594265 + + + + + + + SRR31114287 + GSM8594265_r1 + + + + GSM8594265_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009430 + SAMN44450844 + GSM8594265 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114288 + GSM8594265_r2 + + + + GSM8594265_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009430 + SAMN44450844 + GSM8594265 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496509 + GSM8594264_r1 + + GSM8594264: Ascl1_sample1_rep2_demultiplex_required; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009428 + GSM8594264 + + + + GSM8594264 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009428 + SAMN44450845 + GSM8594264 + + Ascl1_sample1_rep2_demultiplex_required + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_sample1_rep2_demultiplex_required + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009428 + SAMN44450845 + GSM8594264 + + + + + + + SRR31114289 + GSM8594264_r1 + + + + GSM8594264_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009428 + SAMN44450845 + GSM8594264 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114290 + GSM8594264_r2 + + + + GSM8594264_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009428 + SAMN44450845 + GSM8594264 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496508 + GSM8594263_r1 + + GSM8594263: Mycn_control_rep2; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009427 + GSM8594263 + + + + GSM8594263 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009427 + SAMN44450846 + GSM8594263 + + Mycn_control_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Mycn_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009427 + SAMN44450846 + GSM8594263 + + + + + + + SRR31114291 + GSM8594263_r1 + + + + GSM8594263_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009427 + SAMN44450846 + GSM8594263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR31114296 + GSM8594263_r6 + + + + GSM8594263_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009427 + SAMN44450846 + GSM8594263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114297 + GSM8594263_r7 + + + + GSM8594263_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009427 + SAMN44450846 + GSM8594263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496507 + GSM8594262_r1 + + GSM8594262: Mycn_cKO_rep2; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009426 + GSM8594262 + + + + GSM8594262 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + Mycn_cKO_rep2 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Mycn_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + + + + + + SRR31114298 + GSM8594262_r1 + + + + GSM8594262_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR31114302 + GSM8594262_r5 + + + + GSM8594262_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114303 + GSM8594262_r6 + + + + GSM8594262_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114304 + GSM8594262_r7 + + + + GSM8594262_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009426 + SAMN44450847 + GSM8594262 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496506 + GSM8594261_r1 + + GSM8594261: Mycn_control_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009425 + GSM8594261 + + + + GSM8594261 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009425 + SAMN44450848 + GSM8594261 + + Mycn_control_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Mycn_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009425 + SAMN44450848 + GSM8594261 + + + + + + + SRR31114305 + GSM8594261_r1 + + + + GSM8594261_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009425 + SAMN44450848 + GSM8594261 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR31114308 + GSM8594261_r4 + + + + GSM8594261_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009425 + SAMN44450848 + GSM8594261 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26496505 + GSM8594260_r1 + + GSM8594260: Mycn_cKO_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009424 + GSM8594260 + + + + GSM8594260 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009424 + SAMN44450849 + GSM8594260 + + Mycn_cKO_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Mycn_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009424 + SAMN44450849 + GSM8594260 + + + + + + + SRR31114309 + GSM8594260_r1 + + + + GSM8594260_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009424 + SAMN44450849 + GSM8594260 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496504 + GSM8594259_r1 + + GSM8594259: Huwe1_control_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009423 + GSM8594259 + + + + GSM8594259 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009423 + SAMN44450850 + GSM8594259 + + Huwe1_control_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Huwe1_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009423 + SAMN44450850 + GSM8594259 + + + + + + + SRR31114313 + GSM8594259_r1 + + + + GSM8594259_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009423 + SAMN44450850 + GSM8594259 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496503 + GSM8594258_r1 + + GSM8594258: Huwe1_cKO_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009421 + GSM8594258 + + + + GSM8594258 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009421 + SAMN44450851 + GSM8594258 + + Huwe1_cKO_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Huwe1_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009421 + SAMN44450851 + GSM8594258 + + + + + + + SRR31114317 + GSM8594258_r1 + + + + GSM8594258_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009421 + SAMN44450851 + GSM8594258 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496502 + GSM8594257_r1 + + GSM8594257: Ascl1_control_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009422 + GSM8594257 + + + + GSM8594257 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009422 + SAMN44450852 + GSM8594257 + + Ascl1_control_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009422 + SAMN44450852 + GSM8594257 + + + + + + + SRR31114321 + GSM8594257_r1 + + + + GSM8594257_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009422 + SAMN44450852 + GSM8594257 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX26496501 + GSM8594256_r1 + + GSM8594256: Ascl1_cKO_rep1; Mus musculus; RNA-Seq + + + SRP540808 + PRJNA1177781 + + + + + + + SRS23009420 + GSM8594256 + + + + GSM8594256 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Wild type mouse active adult hippocampal neural stem cells (AHNSCs) were cultured in DMEM/F-12 + Glutamax media supplemented with 1x N2, 1x penicillin/streptomycin (ThermoFisher Scientific, 15140), 3 ug/ml laminin (Sigma L2020), 5 ug/ml heparin (Sigma, H3393) and 20ng/ml Fibroblast Growth Factor (PeproTech, 450-33). The ASCL1 CUT & RUN samples (2 replicates) was performed with the CUT & RUN kit. Briefly, 500,000 cultured AHNSCs were collected in a 1.5 ml tube containing wash buffer. The cells were captured with ConA beads and incubated with 0.5 μg of the anti-ASCL1 monoclonal antibody overnight at 4°C in antibody buffer. After washing the unbound antibody, pAG-MNase was added and incubated for 10 min at RT. After washing, CaCl2 was added and incubated for 2 h and the reaction was stopped with the stop buffer. The protein-DNA complexes were released by incubating at 37°C for 10 min. DNA was then purified using a DNA cleanup kit. scRNA-seq: Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer's instructions (10x Genomics Chemistry, Single Cell version 3.0.1). CUT&RUN Sequencing library was prepared using the NEBNext Ultra II DNA library preparation kit for Illumina specifically modified to make libraries from small DNA fragments. Briefly, end repair was conducted at 20°C for 30 min, followed by dA-tailing at 50°C for 60 min. After adapter ligation, the DNA fragments were purified by 1.75X volume of AMPure XP beads followed by 14 cycles PCR amplification with NEBNext Ultra II Q5 Master Mix. The PCR products were firstly cleaned up with 0.8X volume of AMPure XP beads. Then, a second cleaning was performed with 1.2x volume of AMPure XP beads to remove PCR products shorter than 150 base pairs. A final round of 1.2x AMPure XP beads clean-up was performed to eliminate PCR dimers. The library was sequenced on the NovaSeq 6000 instrument, PE100. + + + + + Illumina HiSeq 4000 + + + + + + SRA2111913 + SUB15258249 + + + + Cancer Neuroscience Lab, Cancer Research Program, QIMR Berghofer MRI + +
+ 300 Herston Road + Brisbane + QLD + Australia +
+ + Lachlan + Harris + + + + + + SRP540808 + PRJNA1177781 + GSE280296 + + + Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells. + + Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation. Overall design: Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4?°C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100. **Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025** + GSE280296 + + + + + pubmed + 40498845 + + + + + + + SRS23009420 + SAMN44450853 + GSM8594256 + + Ascl1_cKO_rep1 + + 10090 + Mus musculus + + + + + bioproject + 1177781 + + + + + + + source_name + hippocampal neural stem cells (FLOW-enriched) + + + tissue + hippocampal neural stem cells (FLOW-enriched) + + + genotype + Ascl1_cKO + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23009420 + SAMN44450853 + GSM8594256 + + + + + + + SRR31114332 + GSM8594256_r1 + + + + GSM8594256_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009420 + SAMN44450853 + GSM8594256 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR31114341 + GSM8594256_r8 + + + + GSM8594256_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009420 + SAMN44450853 + GSM8594256 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31114342 + GSM8594256_r9 + + + + GSM8594256_r1 + + + + + loader + fastq-load.py + + + + + + SRS23009420 + SAMN44450853 + GSM8594256 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE283187.xml b/tests/data/GSE283187.xml new file mode 100644 index 0000000..f26181d --- /dev/null +++ b/tests/data/GSE283187.xml @@ -0,0 +1,3044 @@ + + + + + + + SRX26921465 + GSM8657367_r1 + + GSM8657367: cortical brain tissue, Het, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398521 + GSM8657367 + + + + GSM8657367 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398521 + SAMN45105167 + GSM8657367 + + cortical brain tissue, Het, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba heterozygot cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba heterozygote + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398521 + SAMN45105167 + GSM8657367 + + + + + + + SRR31555320 + GSM8657367_r1 + + + + GSM8657367_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398521 + SAMN45105167 + GSM8657367 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921464 + GSM8657366_r1 + + GSM8657366: cortical brain tissue, B6_7_28, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398519 + GSM8657366 + + + + GSM8657366 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398519 + SAMN45105168 + GSM8657366 + + cortical brain tissue, B6_7_28, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + WT cortical cells + + + cell type + all cerebral cortex cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398519 + SAMN45105168 + GSM8657366 + + + + + + + SRR31555321 + GSM8657366_r1 + + + + GSM8657366_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398519 + SAMN45105168 + GSM8657366 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921463 + GSM8657365_r1 + + GSM8657365: cortical brain tissue, Ctr, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398518 + GSM8657365 + + + + GSM8657365 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398518 + SAMN45105169 + GSM8657365 + + cortical brain tissue, Ctr, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + WT cortical cells + + + cell type + all cerebral cortex cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398518 + SAMN45105169 + GSM8657365 + + + + + + + SRR31555322 + GSM8657365_r1 + + + + GSM8657365_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398518 + SAMN45105169 + GSM8657365 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921462 + GSM8657364_r1 + + GSM8657364: cortical brain tissue, B6_control_May27, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398517 + GSM8657364 + + + + GSM8657364 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398517 + SAMN45105170 + GSM8657364 + + cortical brain tissue, B6_control_May27, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + WT cortical cells + + + cell type + all cerebral cortex cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398517 + SAMN45105170 + GSM8657364 + + + + + + + SRR31555323 + GSM8657364_r1 + + + + GSM8657364_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398517 + SAMN45105170 + GSM8657364 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921461 + GSM8657363_r1 + + GSM8657363: cortical brain tissue, B6_control_May20, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398516 + GSM8657363 + + + + GSM8657363 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398516 + SAMN45105171 + GSM8657363 + + cortical brain tissue, B6_control_May20, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + WT cortical cells + + + cell type + all cerebral cortex cells + + + genotype + WT + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398516 + SAMN45105171 + GSM8657363 + + + + + + + SRR31555324 + GSM8657363_r1 + + + + GSM8657363_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398516 + SAMN45105171 + GSM8657363 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921460 + GSM8657362_r1 + + GSM8657362: cortical brain tissue, PD_754 , snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398515 + GSM8657362 + + + + GSM8657362 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398515 + SAMN45105172 + GSM8657362 + + cortical brain tissue, PD_754 , snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + SNCA tg cortical cells + + + cell type + all cerebral cortex cells + + + genotype + SNCA tg + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398515 + SAMN45105172 + GSM8657362 + + + + + + + SRR31555325 + GSM8657362_r1 + + + + GSM8657362_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398515 + SAMN45105172 + GSM8657362 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921459 + GSM8657361_r1 + + GSM8657361: cortical brain tissue, PD_740, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398514 + GSM8657361 + + + + GSM8657361 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398514 + SAMN45105173 + GSM8657361 + + cortical brain tissue, PD_740, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + SNCA tg cortical cells + + + cell type + all cerebral cortex cells + + + genotype + SNCA tg + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398514 + SAMN45105173 + GSM8657361 + + + + + + + SRR31555326 + GSM8657361_r1 + + + + GSM8657361_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398514 + SAMN45105173 + GSM8657361 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921458 + GSM8657360_r1 + + GSM8657360: cortical brain tissue, 729_PD, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398513 + GSM8657360 + + + + GSM8657360 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398513 + SAMN45105174 + GSM8657360 + + cortical brain tissue, 729_PD, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + SNCA tg cortical cells + + + cell type + all cerebral cortex cells + + + genotype + SNCA tg + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398513 + SAMN45105174 + GSM8657360 + + + + + + + SRR31555327 + GSM8657360_r1 + + + + GSM8657360_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398513 + SAMN45105174 + GSM8657360 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921457 + GSM8657359_r1 + + GSM8657359: cortical brain tissue, 201, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398512 + GSM8657359 + + + + GSM8657359 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398512 + SAMN45105175 + GSM8657359 + + cortical brain tissue, 201, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398512 + SAMN45105175 + GSM8657359 + + + + + + + SRR31555328 + GSM8657359_r1 + + + + GSM8657359_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398512 + SAMN45105175 + GSM8657359 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921456 + GSM8657358_r1 + + GSM8657358: cortical brain tissue, 185_GD , snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398511 + GSM8657358 + + + + GSM8657358 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398511 + SAMN45105176 + GSM8657358 + + cortical brain tissue, 185_GD , snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398511 + SAMN45105176 + GSM8657358 + + + + + + + SRR31555329 + GSM8657358_r1 + + + + GSM8657358_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398511 + SAMN45105176 + GSM8657358 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921455 + GSM8657357_r1 + + GSM8657357: cortical brain tissue, 193_GD, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398510 + GSM8657357 + + + + GSM8657357 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398510 + SAMN45105177 + GSM8657357 + + cortical brain tissue, 193_GD, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398510 + SAMN45105177 + GSM8657357 + + + + + + + SRR31555330 + GSM8657357_r1 + + + + GSM8657357_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398510 + SAMN45105177 + GSM8657357 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921454 + GSM8657356_r1 + + GSM8657356: cortical brain tissue, 192_GD, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398509 + GSM8657356 + + + + GSM8657356 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398509 + SAMN45105178 + GSM8657356 + + cortical brain tissue, 192_GD, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398509 + SAMN45105178 + GSM8657356 + + + + + + + SRR31555331 + GSM8657356_r1 + + + + GSM8657356_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398509 + SAMN45105178 + GSM8657356 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921453 + GSM8657355_r1 + + GSM8657355: cortical brain tissue, 184_GP, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398508 + GSM8657355 + + + + GSM8657355 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398508 + SAMN45105179 + GSM8657355 + + cortical brain tissue, 184_GP, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba-SNCA double mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba-SNCA double mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398508 + SAMN45105179 + GSM8657355 + + + + + + + SRR31555332 + GSM8657355_r1 + + + + GSM8657355_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398508 + SAMN45105179 + GSM8657355 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26921452 + GSM8657354_r1 + + GSM8657354: cortical brain tissue, 191_L444P_A30P, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398507 + GSM8657354 + + + + GSM8657354 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398507 + SAMN45105180 + GSM8657354 + + cortical brain tissue, 191_L444P_A30P, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba-SNCA double mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba-SNCA double mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398507 + SAMN45105180 + GSM8657354 + + + + + + + SRR31555333 + GSM8657354_r1 + + + + GSM8657354_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398507 + SAMN45105180 + GSM8657354 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + SRX26921451 + GSM8657353_r1 + + GSM8657353: cortical brain tissue, 187_Mneo-L444P_A30P_May20, snRNA-seq; Mus musculus; RNA-Seq + + + SRP548418 + GSE283187 + + + + + + + SRS23398506 + GSM8657353 + + + + GSM8657353 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer's instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2024666 + SUB14898831 + + + + Chandra Lab, Departments of Neurology and Neuroscience, Yale School of Medicine + +
+ 295 Congress Avenue + New Haven + USA +
+ + Sreeganga + Chandra + + + + + + SRP548418 + PRJNA1192295 + GSE283187 + + + Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies + + GBA mutations are major risk factors for Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB), two common a-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline. Immunohistological analysis revealed cortical phospho-a-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show a-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing a-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through a-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB Overall design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human a-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and a-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression. + GSE283187 + + + + + SRS23398506 + SAMN45105181 + GSM8657353 + + cortical brain tissue, 187_Mneo-L444P_A30P_May20, snRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192295 + + + + + + + source_name + cerebral cortex + + + tissue + cerebral cortex + + + cell line + Gba-SNCA double mutant cortical cells + + + cell type + all cerebral cortex cells + + + genotype + Gba-SNCA double mutant + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23398506 + SAMN45105181 + GSM8657353 + + + + + + + SRR31555334 + GSM8657353_r1 + + + + GSM8657353_r1 + + + + + loader + fastq-load.py + + + + + + SRS23398506 + SAMN45105181 + GSM8657353 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE283268.xml b/tests/data/GSE283268.xml new file mode 100644 index 0000000..7c84da2 --- /dev/null +++ b/tests/data/GSE283268.xml @@ -0,0 +1,3100 @@ + + + + + + + SRX26931808 + GSM8658910_r1 + + GSM8658910: UTX_wk13, replicate 3, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405283 + GSM8658910 + + + + GSM8658910 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405283 + SAMN45125779 + GSM8658910 + + UTX_wk13, replicate 3, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405283 + SAMN45125779 + GSM8658910 + + + + + + + SRR31566180 + GSM8658910_r1 + + + + GSM8658910_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405283 + SAMN45125779 + GSM8658910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566181 + GSM8658910_r2 + + + + GSM8658910_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405283 + SAMN45125779 + GSM8658910 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931807 + GSM8658909_r1 + + GSM8658909: UTX_wk13, replicate 2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405282 + GSM8658909 + + + + GSM8658909 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405282 + SAMN45125780 + GSM8658909 + + UTX_wk13, replicate 2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405282 + SAMN45125780 + GSM8658909 + + + + + + + SRR31566182 + GSM8658909_r1 + + + + GSM8658909_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405282 + SAMN45125780 + GSM8658909 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931806 + GSM8658908_r1 + + GSM8658908: UTX_wk13, replicate 1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405281 + GSM8658908 + + + + GSM8658908 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405281 + SAMN45125781 + GSM8658908 + + UTX_wk13, replicate 1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405281 + SAMN45125781 + GSM8658908 + + + + + + + SRR31566183 + GSM8658908_r1 + + + + GSM8658908_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405281 + SAMN45125781 + GSM8658908 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931805 + GSM8658907_r1 + + GSM8658907: WT_wk13, replicate 3, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405280 + GSM8658907 + + + + GSM8658907 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405280 + SAMN45125782 + GSM8658907 + + WT_wk13, replicate 3, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405280 + SAMN45125782 + GSM8658907 + + + + + + + SRR31566184 + GSM8658907_r1 + + + + GSM8658907_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405280 + SAMN45125782 + GSM8658907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566185 + GSM8658907_r2 + + + + GSM8658907_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405280 + SAMN45125782 + GSM8658907 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931804 + GSM8658906_r1 + + GSM8658906: WT_wk13, replicate 2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405279 + GSM8658906 + + + + GSM8658906 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405279 + SAMN45125783 + GSM8658906 + + WT_wk13, replicate 2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405279 + SAMN45125783 + GSM8658906 + + + + + + + SRR31566186 + GSM8658906_r1 + + + + GSM8658906_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405279 + SAMN45125783 + GSM8658906 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931803 + GSM8658905_r1 + + GSM8658905: WT_wk13, replicate 1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405278 + GSM8658905 + + + + GSM8658905 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405278 + SAMN45125784 + GSM8658905 + + WT_wk13, replicate 1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405278 + SAMN45125784 + GSM8658905 + + + + + + + SRR31566187 + GSM8658905_r1 + + + + GSM8658905_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405278 + SAMN45125784 + GSM8658905 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931802 + GSM8658904_r1 + + GSM8658904: UTX_wk8, replicate 3, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405277 + GSM8658904 + + + + GSM8658904 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405277 + SAMN45125785 + GSM8658904 + + UTX_wk8, replicate 3, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405277 + SAMN45125785 + GSM8658904 + + + + + + + SRR31566188 + GSM8658904_r1 + + + + GSM8658904_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405277 + SAMN45125785 + GSM8658904 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566189 + GSM8658904_r2 + + + + GSM8658904_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405277 + SAMN45125785 + GSM8658904 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931801 + GSM8658903_r1 + + GSM8658903: UTX_wk8, replicate 2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405276 + GSM8658903 + + + + GSM8658903 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405276 + SAMN45125786 + GSM8658903 + + UTX_wk8, replicate 2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405276 + SAMN45125786 + GSM8658903 + + + + + + + SRR31566190 + GSM8658903_r1 + + + + GSM8658903_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405276 + SAMN45125786 + GSM8658903 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566191 + GSM8658903_r2 + + + + GSM8658903_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405276 + SAMN45125786 + GSM8658903 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931800 + GSM8658902_r1 + + GSM8658902: UTX_wk8, replicate 1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405275 + GSM8658902 + + + + GSM8658902 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405275 + SAMN45125787 + GSM8658902 + + UTX_wk8, replicate 1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.UTX-/-LckCre+ + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405275 + SAMN45125787 + GSM8658902 + + + + + + + SRR31566192 + GSM8658902_r1 + + + + GSM8658902_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405275 + SAMN45125787 + GSM8658902 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566193 + GSM8658902_r2 + + + + GSM8658902_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405275 + SAMN45125787 + GSM8658902 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931799 + GSM8658901_r1 + + GSM8658901: WT_wk8, replicate 3, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405274 + GSM8658901 + + + + GSM8658901 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405274 + SAMN45125788 + GSM8658901 + + WT_wk8, replicate 3, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405274 + SAMN45125788 + GSM8658901 + + + + + + + SRR31566194 + GSM8658901_r1 + + + + GSM8658901_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405274 + SAMN45125788 + GSM8658901 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566195 + GSM8658901_r2 + + + + GSM8658901_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405274 + SAMN45125788 + GSM8658901 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931798 + GSM8658900_r1 + + GSM8658900: WT_wk8, replicate 2, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405273 + GSM8658900 + + + + GSM8658900 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405273 + SAMN45125789 + GSM8658900 + + WT_wk8, replicate 2, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405273 + SAMN45125789 + GSM8658900 + + + + + + + SRR31566196 + GSM8658900_r1 + + + + GSM8658900_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405273 + SAMN45125789 + GSM8658900 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566197 + GSM8658900_r2 + + + + GSM8658900_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405273 + SAMN45125789 + GSM8658900 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX26931797 + GSM8658899_r1 + + GSM8658899: WT_wk8, replicate 1, scRNA-seq; Mus musculus; RNA-Seq + + + SRP548652 + GSE283268 + + + + + + + SRS23405272 + GSM8658899 + + + + GSM8658899 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer) Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2025306 + SUB14901890 + + + + Maureen Su, MIMG, University of California, Los Angeles + +
+ 609 Charles E Young Dr E + Los Angeles + CA + USA +
+ + Ho Chung + Chen + + + + + + SRP548652 + PRJNA1192996 + GSE283268 + + + The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors + + Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq. Overall design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile. + GSE283268 + + + + + SRS23405272 + SAMN45125790 + GSM8658899 + + WT_wk8, replicate 1, scRNA-seq + + 10090 + Mus musculus + + + + + bioproject + 1192996 + + + + + + + source_name + pancreatic lymph node + + + tissue + pancreatic lymph node + + + cell type + immune cells + + + genotype + NOD.WT + + + Sex + female + + + disease state + pre-diabetic + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23405272 + SAMN45125790 + GSM8658899 + + + + + + + SRR31566198 + GSM8658899_r1 + + + + GSM8658899_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405272 + SAMN45125790 + GSM8658899 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31566199 + GSM8658899_r2 + + + + GSM8658899_r1 + + + + + loader + fastq-load.py + + + + + + SRS23405272 + SAMN45125790 + GSM8658899 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE284797.xml b/tests/data/GSE284797.xml new file mode 100644 index 0000000..ae8a627 --- /dev/null +++ b/tests/data/GSE284797.xml @@ -0,0 +1,3883 @@ + + + + + + + SRX27201683 + GSM8702688_r1 + + GSM8702688: APP/PS1, KYL, replicate 3, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651838 + GSM8702688 + + + + GSM8702688 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + APP/PS1, KYL, replicate 3, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + KYL + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + + + + + + SRR31841614 + GSM8702688_r1 + + + + GSM8702688_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841615 + GSM8702688_r2 + + + + GSM8702688_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841616 + GSM8702688_r3 + + + + GSM8702688_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841617 + GSM8702688_r4 + + + + GSM8702688_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651838 + SAMN46001251 + GSM8702688 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201682 + GSM8702687_r1 + + GSM8702687: APP/PS1, KYL, replicate 2, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651837 + GSM8702687 + + + + GSM8702687 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + APP/PS1, KYL, replicate 2, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + KYL + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + + + + + + SRR31841618 + GSM8702687_r1 + + + + GSM8702687_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841619 + GSM8702687_r2 + + + + GSM8702687_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841620 + GSM8702687_r3 + + + + GSM8702687_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841621 + GSM8702687_r4 + + + + GSM8702687_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651837 + SAMN46001252 + GSM8702687 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201681 + GSM8702686_r1 + + GSM8702686: APP/PS1, KYL, replicate 1, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651836 + GSM8702686 + + + + GSM8702686 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + APP/PS1, KYL, replicate 1, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + KYL + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + + + + + + SRR31841622 + GSM8702686_r1 + + + + GSM8702686_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841623 + GSM8702686_r2 + + + + GSM8702686_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841624 + GSM8702686_r3 + + + + GSM8702686_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841625 + GSM8702686_r4 + + + + GSM8702686_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651836 + SAMN46001253 + GSM8702686 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201680 + GSM8702685_r1 + + GSM8702685: APP/PS1, aCSF, replicate 3, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651835 + GSM8702685 + + + + GSM8702685 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + APP/PS1, aCSF, replicate 3, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + + + + + + SRR31841626 + GSM8702685_r1 + + + + GSM8702685_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841627 + GSM8702685_r2 + + + + GSM8702685_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841628 + GSM8702685_r3 + + + + GSM8702685_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841637 + GSM8702685_r4 + + + + GSM8702685_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651835 + SAMN46001254 + GSM8702685 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201679 + GSM8702684_r1 + + GSM8702684: APP/PS1, aCSF, replicate 2, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651834 + GSM8702684 + + + + GSM8702684 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + APP/PS1, aCSF, replicate 2, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + + + + + + SRR31841629 + GSM8702684_r1 + + + + GSM8702684_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841630 + GSM8702684_r2 + + + + GSM8702684_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841631 + GSM8702684_r3 + + + + GSM8702684_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841636 + GSM8702684_r4 + + + + GSM8702684_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651834 + SAMN46001255 + GSM8702684 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201678 + GSM8702683_r1 + + GSM8702683: APP/PS1, aCSF, replicate 1, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651833 + GSM8702683 + + + + GSM8702683 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + APP/PS1, aCSF, replicate 1, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + Tg + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + + + + + + SRR31841632 + GSM8702683_r1 + + + + GSM8702683_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841633 + GSM8702683_r2 + + + + GSM8702683_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841634 + GSM8702683_r3 + + + + GSM8702683_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841635 + GSM8702683_r4 + + + + GSM8702683_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651833 + SAMN46001256 + GSM8702683 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201677 + GSM8702682_r1 + + GSM8702682: WT, aCSF, replicate 3, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651831 + GSM8702682 + + + + GSM8702682 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + WT, aCSF, replicate 3, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + WT + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + + + + + + SRR31841638 + GSM8702682_r1 + + + + GSM8702682_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841639 + GSM8702682_r2 + + + + GSM8702682_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841640 + GSM8702682_r3 + + + + GSM8702682_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841641 + GSM8702682_r4 + + + + GSM8702682_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651831 + SAMN46001257 + GSM8702682 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201676 + GSM8702681_r1 + + GSM8702681: WT, aCSF, replicate 2, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651832 + GSM8702681 + + + + GSM8702681 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + WT, aCSF, replicate 2, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + WT + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + + + + + + SRR31841642 + GSM8702681_r1 + + + + GSM8702681_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841643 + GSM8702681_r2 + + + + GSM8702681_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841644 + GSM8702681_r3 + + + + GSM8702681_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841645 + GSM8702681_r4 + + + + GSM8702681_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651832 + SAMN46001258 + GSM8702681 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX27201675 + GSM8702680_r1 + + GSM8702680: WT, aCSF, replicate 1, snRNASeq; Mus musculus; RNA-Seq + + + SRP554128 + GSE284797 + + + + + + + SRS23651830 + GSM8702680 + + + + GSM8702680 + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer's instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2042029 + SUB14958337 + + + + Hong Kong University of Science and Technology + +
+ 广东省深圳市南山区, 南方科技大学第二科研楼401 + 深圳市 + 广东省 + Hong Kong +
+ + Rui + QU + + + + + + SRP554128 + PRJNA1203656 + GSE284797 + + + Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease + + Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cellular-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which are characteristics associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD. Overall design: Hippocampus from aCSF-treated WT, aCSF-treated APP/PS1 mice and KYL-treated APP/PS1 mice + GSE284797 + + + + + pubmed + 39928878 + + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + WT, aCSF, replicate 1, snRNASeq + + 10090 + Mus musculus + + + + + bioproject + 1203656 + + + + + + + source_name + Hippocampi + + + tissue + Hippocampi + + + genotype + WT + + + treatment + aCSF + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + + + + + + SRR31841646 + GSM8702680_r1 + + + + GSM8702680_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841647 + GSM8702680_r2 + + + + GSM8702680_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841648 + GSM8702680_r3 + + + + GSM8702680_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR31841649 + GSM8702680_r4 + + + + GSM8702680_r1 + + + + + loader + fastq-load.py + + + + + + SRS23651830 + SAMN46001259 + GSM8702680 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE287769.xml b/tests/data/GSE287769.xml new file mode 100644 index 0000000..daa2b9d --- /dev/null +++ b/tests/data/GSE287769.xml @@ -0,0 +1,4634 @@ + + + + + + + SRX27438120 + GSM8751069_r1 + + GSM8751069: CC-NfL, replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP559344 + GSE287769 + + + + + + + SRS23865102 + GSM8751069 + + + + GSM8751069 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were deeply anesthetized with 2.5% avertin (2,2,2-tribromoethanol (0.5 ml/25 g body weight) and perfused with ice-cold PBS. Both hippocampi were immediately dissected and chopped into 1-2 mm2 pieces in 2 ml ice-cold Hibernate A minus calcium (HACA, BrainBits). Tissue pieces were collected by centrifuging at 300 x g for 2 min in a round-bottom 2 ml tube and added with enzyme mixes from Neural Tissue Dissociation Kit (P) (Miltenyi 130-092-628) following the manufacturer's manual with slight modifications. Each tissue sample was added into 2 ml pre-warmed Enzyme mix 1 with 5 mg/ml actinomycin D (Sigma-Aldrich A1410) and incubated on a rotator for 15 min at 37C. After adding Enzyme mix 2, samples were gently triturated with wide-orifice pipette tips, incubated for 10 min, gently triturated with regular pipette tips, incubated for another 10 min, and gently triturated with gradual addition of 10 ml ice-cold Hibernate A Low Fluorescence medium (HALF, BrainBits). Cell suspensions were filtered through 70 mm strainers (Miltenyi 130-098-462) and then centrifuged at 300 x g for 10 min at 4C. Cell pellets were carefully resuspended with wide-orifice pipette tips in HALF containing 5% FBS, with Calcein Violet AM (Thermo Fisher C34858) and propidium iodide (Thermo Fisher P1304MP) at 1 mg/ml each for live/dead FACS with BD FacsAria Fusion sorters. Sorted live single cell suspensions were collected into HALF containing 5% FBS. Cell suspensions were adjusted to 2,000 cells/ml by centrifugation at 300 x g for 10 min at 4C and resuspension in HALF containing 5% FBS. Cell viability and density were confirmed again by Trypan Blue staining and counting with Bio-Rad Tc10 counter. The single cell suspensions with viability >75% were proceeded for library preparation. Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics PN-1000121 and PN-1000120) were used for library preparation according to the manufacturer's user guides. Cell-RT mix was prepared to aim for 8,000 cells per sample and applied to Chromium Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626). + + + + + Illumina NovaSeq 6000 + + + + + + SRA2058001 + SUB15027854 + + + + Genentech + +
+ 1 Dna way + South San Francisco + CA + USA +
+ + Kimberle + Shen + + + + + + SRP559344 + PRJNA1214588 + GSE287769 + + + Secreted neurofilament light chain (NfL) after neuronal damage induces myeloid cell activation and neuroinflammation [scRNA-Seq] + + Neurofilament light chain (NfL) is a neuron-specific cytoskeletal protein that provides structural support for axons and is released into the extracellular space following neuronal injury. While NfL has been extensively studied as a disease biomarker, the underlying release mechanisms and role in neurodegeneration remain poorly understood. Here, we find that neurons secrete low baseline levels of NfL, while neuronal damage triggers calpain-driven proteolysis and release of fragmented NfL. Secreted NfL activates microglia cells, which can be blocked with anti-NfL antibodies. We utilize in vivo single-cell RNA sequencing to profile brain cells after injection of recombinant NfL into the mouse hippocampus and find robust macrophage and microglial responses. Consistently, NfL knock-out mice ameliorate microgliosis and delay symptom onset in the SOD1 mouse model of amyotrophic lateral sclerosis (ALS). Our results show that released NfL can activate myeloid cells in the brain and is, thus, a potential therapeutic target for neurodegenerative diseases. Overall design: To examine the effect of exogenous NfL on brain cells in vivo, 11-week-old male mice were bilaterally injected in the hippocampus with either vehicle (n=4), full length NfL (1 mg/ml; n=3) or coiled-coil NfL (1 mg/ml; n=3). After three days, the hippocampi were collected, the cells were dissociated, and live cells were sorted. Single-cell libraries were prepared for further analysis. + GSE287769 + + + + + pubmed + 40056413 + + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + CC-NfL, replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1214588 + + + + + + + source_name + Brain: Hippocampus + + + strain + C57BL/6 + + + tissue + Brain: Hippocampus + + + genotype + WT + + + Sex + male + + + age + 11 weeks old + + + treatment + Coiled-coil NfL + + + batch + b2 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + + + + + + SRR32090013 + GSM8751069_r1 + + + + GSM8751069_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090045 + GSM8751069_r2 + + + + GSM8751069_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090046 + GSM8751069_r3 + + + + GSM8751069_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090047 + GSM8751069_r4 + + + + GSM8751069_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865102 + SAMN46378859 + GSM8751069 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX27438111 + GSM8751060_r1 + + GSM8751060: Vehicle, replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP559344 + GSE287769 + + + + + + + SRS23865093 + GSM8751060 + + + + GSM8751060 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mice were deeply anesthetized with 2.5% avertin (2,2,2-tribromoethanol (0.5 ml/25 g body weight) and perfused with ice-cold PBS. Both hippocampi were immediately dissected and chopped into 1-2 mm2 pieces in 2 ml ice-cold Hibernate A minus calcium (HACA, BrainBits). Tissue pieces were collected by centrifuging at 300 x g for 2 min in a round-bottom 2 ml tube and added with enzyme mixes from Neural Tissue Dissociation Kit (P) (Miltenyi 130-092-628) following the manufacturer's manual with slight modifications. Each tissue sample was added into 2 ml pre-warmed Enzyme mix 1 with 5 mg/ml actinomycin D (Sigma-Aldrich A1410) and incubated on a rotator for 15 min at 37C. After adding Enzyme mix 2, samples were gently triturated with wide-orifice pipette tips, incubated for 10 min, gently triturated with regular pipette tips, incubated for another 10 min, and gently triturated with gradual addition of 10 ml ice-cold Hibernate A Low Fluorescence medium (HALF, BrainBits). Cell suspensions were filtered through 70 mm strainers (Miltenyi 130-098-462) and then centrifuged at 300 x g for 10 min at 4C. Cell pellets were carefully resuspended with wide-orifice pipette tips in HALF containing 5% FBS, with Calcein Violet AM (Thermo Fisher C34858) and propidium iodide (Thermo Fisher P1304MP) at 1 mg/ml each for live/dead FACS with BD FacsAria Fusion sorters. Sorted live single cell suspensions were collected into HALF containing 5% FBS. Cell suspensions were adjusted to 2,000 cells/ml by centrifugation at 300 x g for 10 min at 4C and resuspension in HALF containing 5% FBS. Cell viability and density were confirmed again by Trypan Blue staining and counting with Bio-Rad Tc10 counter. The single cell suspensions with viability >75% were proceeded for library preparation. Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics PN-1000121 and PN-1000120) were used for library preparation according to the manufacturer's user guides. Cell-RT mix was prepared to aim for 8,000 cells per sample and applied to Chromium Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626). + + + + + Illumina NovaSeq 6000 + + + + + + SRA2058001 + SUB15027854 + + + + Genentech + +
+ 1 Dna way + South San Francisco + CA + USA +
+ + Kimberle + Shen + + + + + + SRP559344 + PRJNA1214588 + GSE287769 + + + Secreted neurofilament light chain (NfL) after neuronal damage induces myeloid cell activation and neuroinflammation [scRNA-Seq] + + Neurofilament light chain (NfL) is a neuron-specific cytoskeletal protein that provides structural support for axons and is released into the extracellular space following neuronal injury. While NfL has been extensively studied as a disease biomarker, the underlying release mechanisms and role in neurodegeneration remain poorly understood. Here, we find that neurons secrete low baseline levels of NfL, while neuronal damage triggers calpain-driven proteolysis and release of fragmented NfL. Secreted NfL activates microglia cells, which can be blocked with anti-NfL antibodies. We utilize in vivo single-cell RNA sequencing to profile brain cells after injection of recombinant NfL into the mouse hippocampus and find robust macrophage and microglial responses. Consistently, NfL knock-out mice ameliorate microgliosis and delay symptom onset in the SOD1 mouse model of amyotrophic lateral sclerosis (ALS). Our results show that released NfL can activate myeloid cells in the brain and is, thus, a potential therapeutic target for neurodegenerative diseases. Overall design: To examine the effect of exogenous NfL on brain cells in vivo, 11-week-old male mice were bilaterally injected in the hippocampus with either vehicle (n=4), full length NfL (1 mg/ml; n=3) or coiled-coil NfL (1 mg/ml; n=3). After three days, the hippocampi were collected, the cells were dissociated, and live cells were sorted. Single-cell libraries were prepared for further analysis. + GSE287769 + + + + + pubmed + 40056413 + + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + Vehicle, replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1214588 + + + + + + + source_name + Brain: Hippocampus + + + strain + C57BL/6 + + + tissue + Brain: Hippocampus + + + genotype + WT + + + Sex + male + + + age + 11 weeks old + + + treatment + Vehicle + + + batch + b1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + + + + + + SRR32090044 + GSM8751060_r1 + + + + GSM8751060_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090048 + GSM8751060_r2 + + + + GSM8751060_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090049 + GSM8751060_r3 + + + + GSM8751060_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR32090050 + GSM8751060_r4 + + + + GSM8751060_r1 + + + + + loader + fastq-load.py + + + + + + SRS23865093 + SAMN46378868 + GSM8751060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE295459.xml b/tests/data/GSE295459.xml new file mode 100644 index 0000000..5e97282 --- /dev/null +++ b/tests/data/GSE295459.xml @@ -0,0 +1,2316 @@ + + + + + + + SRX28537271 + GSM8950674_r1 + + GSM8950674: ABX treated APPPS1-21 cortex 4, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838449 + GSM8950674 + + + + GSM8950674 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838449 + SAMN48122920 + GSM8950674 + + ABX treated APPPS1-21 cortex 4, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + ABX + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838449 + SAMN48122920 + GSM8950674 + + + + + + + SRR33292111 + GSM8950674_r1 + + + + GSM8950674_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838449 + SAMN48122920 + GSM8950674 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292112 + GSM8950674_r2 + + + + GSM8950674_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838449 + SAMN48122920 + GSM8950674 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537270 + GSM8950673_r1 + + GSM8950673: ABX treated APPPS1-21 cortex 3, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838448 + GSM8950673 + + + + GSM8950673 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838448 + SAMN48122921 + GSM8950673 + + ABX treated APPPS1-21 cortex 3, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + ABX + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838448 + SAMN48122921 + GSM8950673 + + + + + + + SRR33292113 + GSM8950673_r1 + + + + GSM8950673_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838448 + SAMN48122921 + GSM8950673 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292114 + GSM8950673_r2 + + + + GSM8950673_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838448 + SAMN48122921 + GSM8950673 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537269 + GSM8950672_r1 + + GSM8950672: ABX treated APPPS1-21 cortex 2, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838447 + GSM8950672 + + + + GSM8950672 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838447 + SAMN48122922 + GSM8950672 + + ABX treated APPPS1-21 cortex 2, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + ABX + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838447 + SAMN48122922 + GSM8950672 + + + + + + + SRR33292115 + GSM8950672_r1 + + + + GSM8950672_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838447 + SAMN48122922 + GSM8950672 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292116 + GSM8950672_r2 + + + + GSM8950672_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838447 + SAMN48122922 + GSM8950672 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537268 + GSM8950671_r1 + + GSM8950671: ABX treated APPPS1-21 cortex 1, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838446 + GSM8950671 + + + + GSM8950671 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838446 + SAMN48122923 + GSM8950671 + + ABX treated APPPS1-21 cortex 1, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + ABX + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838446 + SAMN48122923 + GSM8950671 + + + + + + + SRR33292117 + GSM8950671_r1 + + + + GSM8950671_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838446 + SAMN48122923 + GSM8950671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292118 + GSM8950671_r2 + + + + GSM8950671_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838446 + SAMN48122923 + GSM8950671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537267 + GSM8950670_r1 + + GSM8950670: VHL treated APPPS1-21 cortex 4, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838445 + GSM8950670 + + + + GSM8950670 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838445 + SAMN48122924 + GSM8950670 + + VHL treated APPPS1-21 cortex 4, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + Vehicle + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838445 + SAMN48122924 + GSM8950670 + + + + + + + SRR33292119 + GSM8950670_r1 + + + + GSM8950670_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838445 + SAMN48122924 + GSM8950670 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292120 + GSM8950670_r2 + + + + GSM8950670_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838445 + SAMN48122924 + GSM8950670 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537266 + GSM8950669_r1 + + GSM8950669: VHL treated APPPS1-21 cortex 3, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838444 + GSM8950669 + + + + GSM8950669 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838444 + SAMN48122925 + GSM8950669 + + VHL treated APPPS1-21 cortex 3, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + Vehicle + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838444 + SAMN48122925 + GSM8950669 + + + + + + + SRR33292121 + GSM8950669_r1 + + + + GSM8950669_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838444 + SAMN48122925 + GSM8950669 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292122 + GSM8950669_r2 + + + + GSM8950669_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838444 + SAMN48122925 + GSM8950669 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537265 + GSM8950668_r1 + + GSM8950668: VHL treated APPPS1-21 cortex 2, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838443 + GSM8950668 + + + + GSM8950668 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838443 + SAMN48122926 + GSM8950668 + + VHL treated APPPS1-21 cortex 2, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + Vehicle + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838443 + SAMN48122926 + GSM8950668 + + + + + + + SRR33292123 + GSM8950668_r1 + + + + GSM8950668_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838443 + SAMN48122926 + GSM8950668 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292124 + GSM8950668_r2 + + + + GSM8950668_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838443 + SAMN48122926 + GSM8950668 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28537264 + GSM8950667_r1 + + GSM8950667: VHL treated APPPS1-21 cortex 1, snRNA-Seq; Mus musculus; RNA-Seq + + + SRP580864 + PRJNA1254715 + + + + + + + SRS24838442 + GSM8950667 + + + + GSM8950667 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2117725 + SUB15277801 + + + + Northwestern University Feinberg School of Medicine + +
+ Tarry Building Room 8-711 300 E Superior + CHICAGO + IL + USA +
+ + Sidhanth + Chandra + + + + + + SRP580864 + PRJNA1254715 + GSE295459 + + + Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice + + Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis + GSE295459 + + + + + SRS24838442 + SAMN48122927 + GSM8950667 + + VHL treated APPPS1-21 cortex 1, snRNA-Seq + + 10090 + Mus musculus + + + + + bioproject + 1254715 + + + + + + + source_name + Brain cortex + + + tissue + Brain cortex + + + genotype + APPPS1-21 + + + treatment + Vehicle + + + batch + 1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24838442 + SAMN48122927 + GSM8950667 + + + + + + + SRR33292125 + GSM8950667_r1 + + + + GSM8950667_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838442 + SAMN48122927 + GSM8950667 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33292126 + GSM8950667_r2 + + + + GSM8950667_r1 + + + + + loader + fastq-load.py + + + + + + SRS24838442 + SAMN48122927 + GSM8950667 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE296027.xml b/tests/data/GSE296027.xml new file mode 100644 index 0000000..13dcbd1 --- /dev/null +++ b/tests/data/GSE296027.xml @@ -0,0 +1,3642 @@ + + + + + + + SRX28630090 + GSM8963621_r1 + + GSM8963621: Microglia, 5xFAD negative, Csf1 treated, CD11c negative 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901112 + GSM8963621 + + + + GSM8963621 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901112 + SAMN48257705 + GSM8963621 + + Microglia, 5xFAD negative, Csf1 treated, CD11c negative 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD negative, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901112 + SAMN48257705 + GSM8963621 + + + + + + + SRR33387144 + GSM8963621_r1 + + + + GSM8963621_r1 + + + + + + SRS24901112 + SAMN48257705 + GSM8963621 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630089 + GSM8963620_r1 + + GSM8963620: Microglia, 5xFAD negative, Csf1 treated, CD11c negative 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901111 + GSM8963620 + + + + GSM8963620 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901111 + SAMN48257706 + GSM8963620 + + Microglia, 5xFAD negative, Csf1 treated, CD11c negative 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD negative, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901111 + SAMN48257706 + GSM8963620 + + + + + + + SRR33387145 + GSM8963620_r1 + + + + GSM8963620_r1 + + + + + + SRS24901111 + SAMN48257706 + GSM8963620 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630088 + GSM8963619_r1 + + GSM8963619: Microglia, 5xFAD negative, PBS control, CD11c negative 3; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901110 + GSM8963619 + + + + GSM8963619 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901110 + SAMN48257707 + GSM8963619 + + Microglia, 5xFAD negative, PBS control, CD11c negative 3 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD negative, PBS control, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901110 + SAMN48257707 + GSM8963619 + + + + + + + SRR33387146 + GSM8963619_r1 + + + + GSM8963619_r1 + + + + + + SRS24901110 + SAMN48257707 + GSM8963619 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630087 + GSM8963618_r1 + + GSM8963618: Microglia, 5xFAD negative, PBS control, CD11c negative 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901109 + GSM8963618 + + + + GSM8963618 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901109 + SAMN48257708 + GSM8963618 + + Microglia, 5xFAD negative, PBS control, CD11c negative 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD negative, PBS control, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901109 + SAMN48257708 + GSM8963618 + + + + + + + SRR33387147 + GSM8963618_r1 + + + + GSM8963618_r1 + + + + + + SRS24901109 + SAMN48257708 + GSM8963618 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630086 + GSM8963617_r1 + + GSM8963617: Microglia, 5xFAD negative, PBS control, CD11c negative 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901108 + GSM8963617 + + + + GSM8963617 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901108 + SAMN48257710 + GSM8963617 + + Microglia, 5xFAD negative, PBS control, CD11c negative 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD negative, PBS control, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901108 + SAMN48257710 + GSM8963617 + + + + + + + SRR33387148 + GSM8963617_r1 + + + + GSM8963617_r1 + + + + + + SRS24901108 + SAMN48257710 + GSM8963617 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630085 + GSM8963616_r1 + + GSM8963616: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 4; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901107 + GSM8963616 + + + + GSM8963616 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901107 + SAMN48257711 + GSM8963616 + + Microglia, 5xFAD positive, Csf1 treated, CD11c positive 4 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901107 + SAMN48257711 + GSM8963616 + + + + + + + SRR33387149 + GSM8963616_r1 + + + + GSM8963616_r1 + + + + + + SRS24901107 + SAMN48257711 + GSM8963616 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630084 + GSM8963615_r1 + + GSM8963615: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 3; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901106 + GSM8963615 + + + + GSM8963615 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901106 + SAMN48257712 + GSM8963615 + + Microglia, 5xFAD positive, Csf1 treated, CD11c positive 3 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901106 + SAMN48257712 + GSM8963615 + + + + + + + SRR33387150 + GSM8963615_r1 + + + + GSM8963615_r1 + + + + + + SRS24901106 + SAMN48257712 + GSM8963615 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630083 + GSM8963614_r1 + + GSM8963614: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901105 + GSM8963614 + + + + GSM8963614 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901105 + SAMN48257713 + GSM8963614 + + Microglia, 5xFAD positive, Csf1 treated, CD11c positive 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901105 + SAMN48257713 + GSM8963614 + + + + + + + SRR33387151 + GSM8963614_r1 + + + + GSM8963614_r1 + + + + + + SRS24901105 + SAMN48257713 + GSM8963614 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630082 + GSM8963613_r1 + + GSM8963613: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901104 + GSM8963613 + + + + GSM8963613 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901104 + SAMN48257715 + GSM8963613 + + Microglia, 5xFAD positive, Csf1 treated, CD11c positive 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901104 + SAMN48257715 + GSM8963613 + + + + + + + SRR33387152 + GSM8963613_r1 + + + + GSM8963613_r1 + + + + + + SRS24901104 + SAMN48257715 + GSM8963613 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630081 + GSM8963612_r1 + + GSM8963612: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 4; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901103 + GSM8963612 + + + + GSM8963612 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901103 + SAMN48257716 + GSM8963612 + + Microglia, 5xFAD positive, Csf1 treated, CD11c negative 4 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901103 + SAMN48257716 + GSM8963612 + + + + + + + SRR33387153 + GSM8963612_r1 + + + + GSM8963612_r1 + + + + + + SRS24901103 + SAMN48257716 + GSM8963612 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630080 + GSM8963611_r1 + + GSM8963611: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 3; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901102 + GSM8963611 + + + + GSM8963611 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901102 + SAMN48257717 + GSM8963611 + + Microglia, 5xFAD positive, Csf1 treated, CD11c negative 3 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901102 + SAMN48257717 + GSM8963611 + + + + + + + SRR33387154 + GSM8963611_r1 + + + + GSM8963611_r1 + + + + + + SRS24901102 + SAMN48257717 + GSM8963611 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630079 + GSM8963610_r1 + + GSM8963610: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901101 + GSM8963610 + + + + GSM8963610 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901101 + SAMN48257718 + GSM8963610 + + Microglia, 5xFAD positive, Csf1 treated, CD11c negative 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901101 + SAMN48257718 + GSM8963610 + + + + + + + SRR33387155 + GSM8963610_r1 + + + + GSM8963610_r1 + + + + + + SRS24901101 + SAMN48257718 + GSM8963610 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630078 + GSM8963609_r1 + + GSM8963609: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901100 + GSM8963609 + + + + GSM8963609 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901100 + SAMN48257719 + GSM8963609 + + Microglia, 5xFAD positive, Csf1 treated, CD11c negative 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + mCSF + + + library type + mRNA + + + sample group + 5xFAD positive, Csf1 treated, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901100 + SAMN48257719 + GSM8963609 + + + + + + + SRR33387156 + GSM8963609_r1 + + + + GSM8963609_r1 + + + + + + SRS24901100 + SAMN48257719 + GSM8963609 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630077 + GSM8963608_r1 + + GSM8963608: Microglia, 5xFAD positive, PBS control, CD11c positive 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901099 + GSM8963608 + + + + GSM8963608 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901099 + SAMN48257720 + GSM8963608 + + Microglia, 5xFAD positive, PBS control, CD11c positive 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD positive, PBS control, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901099 + SAMN48257720 + GSM8963608 + + + + + + + SRR33387157 + GSM8963608_r1 + + + + GSM8963608_r1 + + + + + + SRS24901099 + SAMN48257720 + GSM8963608 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630076 + GSM8963607_r1 + + GSM8963607: Microglia, 5xFAD positive, PBS control, CD11c positive 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901098 + GSM8963607 + + + + GSM8963607 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901098 + SAMN48257721 + GSM8963607 + + Microglia, 5xFAD positive, PBS control, CD11c positive 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD positive, PBS control, CD11c positive + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901098 + SAMN48257721 + GSM8963607 + + + + + + + SRR33387158 + GSM8963607_r1 + + + + GSM8963607_r1 + + + + + + SRS24901098 + SAMN48257721 + GSM8963607 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630075 + GSM8963606_r1 + + GSM8963606: Microglia, 5xFAD positive, PBS control, CD11c negative 2; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901097 + GSM8963606 + + + + GSM8963606 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901097 + SAMN48257722 + GSM8963606 + + Microglia, 5xFAD positive, PBS control, CD11c negative 2 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD positive, PBS control, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901097 + SAMN48257722 + GSM8963606 + + + + + + + SRR33387159 + GSM8963606_r1 + + + + GSM8963606_r1 + + + + + + SRS24901097 + SAMN48257722 + GSM8963606 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28630074 + GSM8963605_r1 + + GSM8963605: Microglia, 5xFAD positive, PBS control, CD11c negative 1; Mus musculus; RNA-Seq + + + SRP582403 + GSE296027 + + + + + + + SRS24901096 + GSM8963605 + + + + GSM8963605 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend #100330, Gr1 cloneRB6-8C5, BioLegend #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj). Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA. For RNA sequencing, the mCEL-Seq2 protocol was used as previously established. + + + + + Illumina HiSeq 2000 + + + + + + SRA2121488 + SUB15292960 + + + + Institut für Neuropathologie, Universitätsklinikum Freiburg + +
+ Breisacher Str. 64, C/O Institut für Neuropathologie + Freiburg im Breisgau + Baden-Württemberg + Germany +
+ + Marco + Prinz + + + + + + SRP582403 + PRJNA1257351 + GSE296027 + + + Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq2_Csf1] + + Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration. Overall design: Following either colony stimulating factor 1 (Csf1) or PBS (control) treatment, microglia from early stage (ES) 5xFAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq. + GSE296027 + + + + + pubmed + 40659845 + + + + + + + SRS24901096 + SAMN48257723 + GSM8963605 + + Microglia, 5xFAD positive, PBS control, CD11c negative 1 + + 10090 + Mus musculus + + + + + bioproject + 1257351 + + + + + + + source_name + Brain + + + tissue + Brain + + + cell type + Microglia + + + genotype + Cx3cr1-CreERT2 R26-Confetti FAD + + + treatment + PBS + + + library type + mRNA + + + sample group + 5xFAD positive, PBS control, CD11c negative + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS24901096 + SAMN48257723 + GSM8963605 + + + + + + + SRR33387160 + GSM8963605_r1 + + + + GSM8963605_r1 + + + + + + SRS24901096 + SAMN48257723 + GSM8963605 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE297666.xml b/tests/data/GSE297666.xml new file mode 100644 index 0000000..61eeea7 --- /dev/null +++ b/tests/data/GSE297666.xml @@ -0,0 +1,1114 @@ + + + + + + + SRX28870427 + GSM8996338_r1 + + GSM8996338: TRPM2 Mg KO+Bilirubin 2; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097764 + GSM8996338 + + + + GSM8996338 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097764 + SAMN48625788 + GSM8996338 + + TRPM2 Mg KO+Bilirubin 2 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097764 + SAMN48625788 + GSM8996338 + + + + + + + SRR33642800 + GSM8996338_r1 + + + + GSM8996338_r1 + + + + + + SRS25097764 + SAMN48625788 + GSM8996338 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28870426 + GSM8996337_r1 + + GSM8996337: TRPM2 Mg KO+Bilirubin 1; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097763 + GSM8996337 + + + + GSM8996337 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097763 + SAMN48625789 + GSM8996337 + + TRPM2 Mg KO+Bilirubin 1 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097763 + SAMN48625789 + GSM8996337 + + + + + + + SRR33642801 + GSM8996337_r1 + + + + GSM8996337_r1 + + + + + + SRS25097763 + SAMN48625789 + GSM8996337 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28870425 + GSM8996336_r1 + + GSM8996336: WT+Bilirubin 2; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097762 + GSM8996336 + + + + GSM8996336 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097762 + SAMN48625790 + GSM8996336 + + WT+Bilirubin 2 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097762 + SAMN48625790 + GSM8996336 + + + + + + + SRR33642802 + GSM8996336_r1 + + + + GSM8996336_r1 + + + + + + SRS25097762 + SAMN48625790 + GSM8996336 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28870424 + GSM8996335_r1 + + GSM8996335: WT+Bilirubin 1; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097760 + GSM8996335 + + + + GSM8996335 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097760 + SAMN48625791 + GSM8996335 + + WT+Bilirubin 1 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097760 + SAMN48625791 + GSM8996335 + + + + + + + SRR33642803 + GSM8996335_r1 + + + + GSM8996335_r1 + + + + + + SRS25097760 + SAMN48625791 + GSM8996335 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28870423 + GSM8996334_r1 + + GSM8996334: WT+Vehicle 2; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097761 + GSM8996334 + + + + GSM8996334 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097761 + SAMN48625792 + GSM8996334 + + WT+Vehicle 2 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097761 + SAMN48625792 + GSM8996334 + + + + + + + SRR33642804 + GSM8996334_r1 + + + + GSM8996334_r1 + + + + + + SRS25097761 + SAMN48625792 + GSM8996334 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX28870422 + GSM8996333_r1 + + GSM8996333: WT+Vehicle 1; Mus musculus; RNA-Seq + + + SRP586600 + GSE297666 + + + + + + + SRS25097759 + GSM8996333 + + + + GSM8996333 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2133271 + SUB15334111 + + + + Department of Anesthesiology,First Affiliated Hospital of USTC + +
+ The First Affiliated Hospital of USTC + Hefei + China +
+ + Shuaijie + Sun + + + + + + SRP586600 + PRJNA1265653 + GSE297666 + + + Research on the role and mechanism of stress liver regulation of negative emotions + + Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies. Overall design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer's protocol of Chromium Next GEM Single Cell 3' Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode. + GSE297666 + + + + + SRS25097759 + SAMN48625793 + GSM8996333 + + WT+Vehicle 1 + + 10090 + Mus musculus + + + + + bioproject + 1265653 + + + + + + + source_name + brain cells + + + cell type + brain cells + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25097759 + SAMN48625793 + GSM8996333 + + + + + + + SRR33642805 + GSM8996333_r1 + + + + GSM8996333_r1 + + + + + + SRS25097759 + SAMN48625793 + GSM8996333 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE297721.xml b/tests/data/GSE297721.xml new file mode 100644 index 0000000..c4a6ae6 --- /dev/null +++ b/tests/data/GSE297721.xml @@ -0,0 +1,12760 @@ + + + + + + + SRX28917237 + GSM8997430_r1 + + GSM8997430: LG852-NY-258; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142175 + GSM8997430 + + + + GSM8997430 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142175 + SAMN48721138 + GSM8997430 + + LG852-NY-258 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.17763157894737 + + + genotype + ApoE3WT;NTG + + + treatment + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142175 + SAMN48721138 + GSM8997430 + + + + + + + SRR33691633 + GSM8997430_r1 + + + + GSM8997430_r1 + + + + + + SRS25142175 + SAMN48721138 + GSM8997430 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR33691634 + GSM8997430_r2 + + + + GSM8997430_r1 + + + + + + SRS25142175 + SAMN48721138 + GSM8997430 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917236 + GSM8997429_r1 + + GSM8997429: LG852-NY-257; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142174 + GSM8997429 + + + + GSM8997429 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142174 + SAMN48721139 + GSM8997429 + + LG852-NY-257 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.17763157894737 + + + genotype + ApoE3WT;P301S Tau+ + + + treatment + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142174 + SAMN48721139 + GSM8997429 + + + + + + + SRR33691637 + GSM8997429_r1 + + + + GSM8997429_r1 + + + + + + SRS25142174 + SAMN48721139 + GSM8997429 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917235 + GSM8997428_r1 + + GSM8997428: LG852-NY-256; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142173 + GSM8997428 + + + + GSM8997428 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142173 + SAMN48721140 + GSM8997428 + + LG852-NY-256 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.17763157894737 + + + genotype + ApoE3WT;P301S Tau+ + + + treatment + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142173 + SAMN48721140 + GSM8997428 + + + + + + + SRR33691640 + GSM8997428_r1 + + + + GSM8997428_r1 + + + + + + SRS25142173 + SAMN48721140 + GSM8997428 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917234 + GSM8997427_r1 + + GSM8997427: LG852-NY-252; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142172 + GSM8997427 + + + + GSM8997427 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142172 + SAMN48721141 + GSM8997427 + + LG852-NY-252 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.27631578947368 + + + genotype + ApoE3WT;NTG + + + treatment + TDI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142172 + SAMN48721141 + GSM8997427 + + + + + + + SRR33691643 + GSM8997427_r1 + + + + GSM8997427_r1 + + + + + + SRS25142172 + SAMN48721141 + GSM8997427 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917233 + GSM8997426_r1 + + GSM8997426: LG852-NY-251; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142171 + GSM8997426 + + + + GSM8997426 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142171 + SAMN48721142 + GSM8997426 + + LG852-NY-251 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.27631578947368 + + + genotype + ApoE3WT;P301S Tau+ + + + treatment + TDI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142171 + SAMN48721142 + GSM8997426 + + + + + + + SRR33691646 + GSM8997426_r1 + + + + GSM8997426_r1 + + + + + + SRS25142171 + SAMN48721142 + GSM8997426 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917232 + GSM8997425_r1 + + GSM8997425: LG852-NY-250; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142170 + GSM8997425 + + + + GSM8997425 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142170 + SAMN48721143 + GSM8997425 + + LG852-NY-250 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.86842105263158 + + + genotype + ApoE3WT;NTG + + + treatment + Control + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142170 + SAMN48721143 + GSM8997425 + + + + + + + SRR33691649 + GSM8997425_r1 + + + + GSM8997425_r1 + + + + + + SRS25142170 + SAMN48721143 + GSM8997425 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917231 + GSM8997424_r1 + + GSM8997424: LG852-NY-244; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142169 + GSM8997424 + + + + GSM8997424 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142169 + SAMN48721144 + GSM8997424 + + LG852-NY-244 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 10.6578947368421 + + + genotype + ApoE3WT;NTG + + + treatment + TDI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142169 + SAMN48721144 + GSM8997424 + + + + + + + SRR33691652 + GSM8997424_r1 + + + + GSM8997424_r1 + + + + + + SRS25142169 + SAMN48721144 + GSM8997424 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917210 + GSM8997404_r1 + + GSM8997404: LG851-NY-150; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142148 + GSM8997404 + + + + GSM8997404 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142148 + SAMN48721164 + GSM8997404 + + LG851-NY-150 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 9.08 + + + genotype + ApoE3CC;P301S Tau+ + + + treatment + N/A + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142148 + SAMN48721164 + GSM8997404 + + + + + + + SRR33691741 + GSM8997404_r1 + + + + GSM8997404_r1 + + + + + + SRS25142148 + SAMN48721164 + GSM8997404 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917209 + GSM8997403_r1 + + GSM8997403: LG851-NY-143; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142147 + GSM8997403 + + + + GSM8997403 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142147 + SAMN48721165 + GSM8997403 + + LG851-NY-143 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 8.95 + + + genotype + ApoE3CC;NTG + + + treatment + N/A + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142147 + SAMN48721165 + GSM8997403 + + + + + + + SRR33691747 + GSM8997403_r1 + + + + GSM8997403_r1 + + + + + + SRS25142147 + SAMN48721165 + GSM8997403 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + SRX28917208 + GSM8997402_r1 + + GSM8997402: LG851-NY-142; Mus musculus; RNA-Seq + + + SRP587458 + GSE297721 + + + + + + + SRS25142146 + GSM8997402 + + + + GSM8997402 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Nuclei isolation adapted from Grubman et al. 2019 Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) + + + + + Illumina NovaSeq 6000 + + + + + + SRA2136125 + SUB15343567 + + + + Gan lab, Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine + + + + SRP587458 + PRJNA1265955 + GSE297721 + + + APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition + + The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy. Overall design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology + GSE297721 + + + + + SRS25142146 + SAMN48721166 + GSM8997402 + + LG851-NY-142 + + 10090 + Mus musculus + + + + + bioproject + 1265955 + + + + + + + source_name + brain hippocampus + + + tissue + brain hippocampus + + + Sex + male + + + age + 8.95 + + + genotype + ApoE3CC;NTG + + + treatment + N/A + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25142146 + SAMN48721166 + GSM8997402 + + + + + + + SRR33691753 + GSM8997402_r1 + + + + GSM8997402_r1 + + + + + + SRS25142146 + SAMN48721166 + GSM8997402 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + SRR33691758 + GSM8997402_r6 + + + + GSM8997402_r1 + + + + + + SRS25142146 + SAMN48721166 + GSM8997402 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE302153.xml b/tests/data/GSE302153.xml new file mode 100644 index 0000000..8f64422 --- /dev/null +++ b/tests/data/GSE302153.xml @@ -0,0 +1,6436 @@ + + + + + + + SRX29604802 + GSM9097158_r1 + + GSM9097158: Sample 32 Control, Ventral, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726202 + GSM9097158 + + + + GSM9097158 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726202 + SAMN49879642 + GSM9097158 + + Sample 32 Control, Ventral, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726202 + SAMN49879642 + GSM9097158 + + + + + + + SRR34444196 + GSM9097158_r1 + + + + GSM9097158_r1 + + + + + + SRS25726202 + SAMN49879642 + GSM9097158 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604801 + GSM9097157_r1 + + GSM9097157: Sample 31 Control, Dorsal, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726201 + GSM9097157 + + + + GSM9097157 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726201 + SAMN49879643 + GSM9097157 + + Sample 31 Control, Dorsal, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726201 + SAMN49879643 + GSM9097157 + + + + + + + SRR34444197 + GSM9097157_r1 + + + + GSM9097157_r1 + + + + + + SRS25726201 + SAMN49879643 + GSM9097157 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604800 + GSM9097156_r1 + + GSM9097156: Sample 30 5xFAD, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726200 + GSM9097156 + + + + GSM9097156 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726200 + SAMN49879644 + GSM9097156 + + Sample 30 5xFAD, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726200 + SAMN49879644 + GSM9097156 + + + + + + + SRR34444198 + GSM9097156_r1 + + + + GSM9097156_r1 + + + + + + SRS25726200 + SAMN49879644 + GSM9097156 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604799 + GSM9097155_r1 + + GSM9097155: Sample 29 5xFAD, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726199 + GSM9097155 + + + + GSM9097155 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726199 + SAMN49879645 + GSM9097155 + + Sample 29 5xFAD, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726199 + SAMN49879645 + GSM9097155 + + + + + + + SRR34444199 + GSM9097155_r1 + + + + GSM9097155_r1 + + + + + + SRS25726199 + SAMN49879645 + GSM9097155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604798 + GSM9097154_r1 + + GSM9097154: Sample 28 Control, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726198 + GSM9097154 + + + + GSM9097154 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726198 + SAMN49879646 + GSM9097154 + + Sample 28 Control, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726198 + SAMN49879646 + GSM9097154 + + + + + + + SRR34444200 + GSM9097154_r1 + + + + GSM9097154_r1 + + + + + + SRS25726198 + SAMN49879646 + GSM9097154 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604797 + GSM9097153_r1 + + GSM9097153: Sample 27 Control, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726197 + GSM9097153 + + + + GSM9097153 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726197 + SAMN49879647 + GSM9097153 + + Sample 27 Control, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726197 + SAMN49879647 + GSM9097153 + + + + + + + SRR34444201 + GSM9097153_r1 + + + + GSM9097153_r1 + + + + + + SRS25726197 + SAMN49879647 + GSM9097153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604796 + GSM9097152_r1 + + GSM9097152: Sample 26 5xFAD, Ventral, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726196 + GSM9097152 + + + + GSM9097152 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726196 + SAMN49879648 + GSM9097152 + + Sample 26 5xFAD, Ventral, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726196 + SAMN49879648 + GSM9097152 + + + + + + + SRR34444202 + GSM9097152_r1 + + + + GSM9097152_r1 + + + + + + SRS25726196 + SAMN49879648 + GSM9097152 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604795 + GSM9097143_r1 + + GSM9097143: Sample 17 5xFAD, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726194 + GSM9097143 + + + + GSM9097143 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726194 + SAMN49879657 + GSM9097143 + + Sample 17 5xFAD, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726194 + SAMN49879657 + GSM9097143 + + + + + + + SRR34444203 + GSM9097143_r1 + + + + GSM9097143_r1 + + + + + + SRS25726194 + SAMN49879657 + GSM9097143 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604794 + GSM9097142_r1 + + GSM9097142: Sample 16 Control, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726195 + GSM9097142 + + + + GSM9097142 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726195 + SAMN49879658 + GSM9097142 + + Sample 16 Control, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726195 + SAMN49879658 + GSM9097142 + + + + + + + SRR34444204 + GSM9097142_r1 + + + + GSM9097142_r1 + + + + + + SRS25726195 + SAMN49879658 + GSM9097142 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604793 + GSM9097141_r1 + + GSM9097141: Sample 15 Control, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726193 + GSM9097141 + + + + GSM9097141 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726193 + SAMN49879659 + GSM9097141 + + Sample 15 Control, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726193 + SAMN49879659 + GSM9097141 + + + + + + + SRR34444205 + GSM9097141_r1 + + + + GSM9097141_r1 + + + + + + SRS25726193 + SAMN49879659 + GSM9097141 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604792 + GSM9097140_r1 + + GSM9097140: Sample 14 Control, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726192 + GSM9097140 + + + + GSM9097140 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726192 + SAMN49879660 + GSM9097140 + + Sample 14 Control, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726192 + SAMN49879660 + GSM9097140 + + + + + + + SRR34444206 + GSM9097140_r1 + + + + GSM9097140_r1 + + + + + + SRS25726192 + SAMN49879660 + GSM9097140 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604791 + GSM9097139_r1 + + GSM9097139: Sample 13 Control, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726191 + GSM9097139 + + + + GSM9097139 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726191 + SAMN49879661 + GSM9097139 + + Sample 13 Control, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726191 + SAMN49879661 + GSM9097139 + + + + + + + SRR34444207 + GSM9097139_r1 + + + + GSM9097139_r1 + + + + + + SRS25726191 + SAMN49879661 + GSM9097139 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604790 + GSM9097138_r1 + + GSM9097138: Sample 12 Control, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726190 + GSM9097138 + + + + GSM9097138 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + NextSeq 2000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726190 + SAMN49879662 + GSM9097138 + + Sample 12 Control, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726190 + SAMN49879662 + GSM9097138 + + + + + + + SRR34444208 + GSM9097138_r1 + + + + GSM9097138_r1 + + + + + + SRS25726190 + SAMN49879662 + GSM9097138 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604789 + GSM9097137_r1 + + GSM9097137: Sample 11 Control, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726189 + GSM9097137 + + + + GSM9097137 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726189 + SAMN49879663 + GSM9097137 + + Sample 11 Control, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726189 + SAMN49879663 + GSM9097137 + + + + + + + SRR34444209 + GSM9097137_r1 + + + + GSM9097137_r1 + + + + + + SRS25726189 + SAMN49879663 + GSM9097137 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604788 + GSM9097136_r1 + + GSM9097136: Sample 10 Control, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726188 + GSM9097136 + + + + GSM9097136 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726188 + SAMN49879664 + GSM9097136 + + Sample 10 Control, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726188 + SAMN49879664 + GSM9097136 + + + + + + + SRR34444210 + GSM9097136_r1 + + + + GSM9097136_r1 + + + + + + SRS25726188 + SAMN49879664 + GSM9097136 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604787 + GSM9097151_r1 + + GSM9097151: Sample 25 5xFAD, Dorsal, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726187 + GSM9097151 + + + + GSM9097151 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726187 + SAMN49879649 + GSM9097151 + + Sample 25 5xFAD, Dorsal, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726187 + SAMN49879649 + GSM9097151 + + + + + + + SRR34444211 + GSM9097151_r1 + + + + GSM9097151_r1 + + + + + + SRS25726187 + SAMN49879649 + GSM9097151 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604786 + GSM9097150_r1 + + GSM9097150: Sample 24 5xFAD, Ventral, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726186 + GSM9097150 + + + + GSM9097150 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726186 + SAMN49879650 + GSM9097150 + + Sample 24 5xFAD, Ventral, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726186 + SAMN49879650 + GSM9097150 + + + + + + + SRR34444212 + GSM9097150_r1 + + + + GSM9097150_r1 + + + + + + SRS25726186 + SAMN49879650 + GSM9097150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604785 + GSM9097149_r1 + + GSM9097149: Sample 23 5xFAD, Dorsal, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726185 + GSM9097149 + + + + GSM9097149 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726185 + SAMN49879651 + GSM9097149 + + Sample 23 5xFAD, Dorsal, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726185 + SAMN49879651 + GSM9097149 + + + + + + + SRR34444213 + GSM9097149_r1 + + + + GSM9097149_r1 + + + + + + SRS25726185 + SAMN49879651 + GSM9097149 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604784 + GSM9097148_r1 + + GSM9097148: Sample 22 Control, Ventral, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726184 + GSM9097148 + + + + GSM9097148 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726184 + SAMN49879652 + GSM9097148 + + Sample 22 Control, Ventral, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726184 + SAMN49879652 + GSM9097148 + + + + + + + SRR34444214 + GSM9097148_r1 + + + + GSM9097148_r1 + + + + + + SRS25726184 + SAMN49879652 + GSM9097148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604783 + GSM9097147_r1 + + GSM9097147: Sample 21 Control, Dorsal, 22 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726183 + GSM9097147 + + + + GSM9097147 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726183 + SAMN49879653 + GSM9097147 + + Sample 21 Control, Dorsal, 22 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 22 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726183 + SAMN49879653 + GSM9097147 + + + + + + + SRR34444215 + GSM9097147_r1 + + + + GSM9097147_r1 + + + + + + SRS25726183 + SAMN49879653 + GSM9097147 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604782 + GSM9097146_r1 + + GSM9097146: Sample 20 5xFAD, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726182 + GSM9097146 + + + + GSM9097146 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726182 + SAMN49879654 + GSM9097146 + + Sample 20 5xFAD, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726182 + SAMN49879654 + GSM9097146 + + + + + + + SRR34444216 + GSM9097146_r1 + + + + GSM9097146_r1 + + + + + + SRS25726182 + SAMN49879654 + GSM9097146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604781 + GSM9097145_r1 + + GSM9097145: Sample 19 5xFAD, Dorsal, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726181 + GSM9097145 + + + + GSM9097145 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726181 + SAMN49879655 + GSM9097145 + + Sample 19 5xFAD, Dorsal, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726181 + SAMN49879655 + GSM9097145 + + + + + + + SRR34444217 + GSM9097145_r1 + + + + GSM9097145_r1 + + + + + + SRS25726181 + SAMN49879655 + GSM9097145 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604780 + GSM9097144_r1 + + GSM9097144: Sample 18 5xFAD, Ventral, 16 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726180 + GSM9097144 + + + + GSM9097144 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726180 + SAMN49879656 + GSM9097144 + + Sample 18 5xFAD, Ventral, 16 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 16 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726180 + SAMN49879656 + GSM9097144 + + + + + + + SRR34444218 + GSM9097144_r1 + + + + GSM9097144_r1 + + + + + + SRS25726180 + SAMN49879656 + GSM9097144 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604779 + GSM9097135_r1 + + GSM9097135: Sample 9 Control, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726178 + GSM9097135 + + + + GSM9097135 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726178 + SAMN49879665 + GSM9097135 + + Sample 9 Control, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726178 + SAMN49879665 + GSM9097135 + + + + + + + SRR34444219 + GSM9097135_r1 + + + + GSM9097135_r1 + + + + + + SRS25726178 + SAMN49879665 + GSM9097135 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604778 + GSM9097134_r1 + + GSM9097134: Sample 8 5xFAD, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726177 + GSM9097134 + + + + GSM9097134 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726177 + SAMN49879666 + GSM9097134 + + Sample 8 5xFAD, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726177 + SAMN49879666 + GSM9097134 + + + + + + + SRR34444220 + GSM9097134_r1 + + + + GSM9097134_r1 + + + + + + SRS25726177 + SAMN49879666 + GSM9097134 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604777 + GSM9097133_r1 + + GSM9097133: Sample 7 5xFAD, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726179 + GSM9097133 + + + + GSM9097133 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726179 + SAMN49879667 + GSM9097133 + + Sample 7 5xFAD, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726179 + SAMN49879667 + GSM9097133 + + + + + + + SRR34444221 + GSM9097133_r1 + + + + GSM9097133_r1 + + + + + + SRS25726179 + SAMN49879667 + GSM9097133 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604776 + GSM9097132_r1 + + GSM9097132: Sample 6 5xFAD, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726176 + GSM9097132 + + + + GSM9097132 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726176 + SAMN49879668 + GSM9097132 + + Sample 6 5xFAD, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726176 + SAMN49879668 + GSM9097132 + + + + + + + SRR34444222 + GSM9097132_r1 + + + + GSM9097132_r1 + + + + + + SRS25726176 + SAMN49879668 + GSM9097132 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604775 + GSM9097131_r1 + + GSM9097131: Sample 5 5xFAD, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726175 + GSM9097131 + + + + GSM9097131 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726175 + SAMN49879669 + GSM9097131 + + Sample 5 5xFAD, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726175 + SAMN49879669 + GSM9097131 + + + + + + + SRR34444223 + GSM9097131_r1 + + + + GSM9097131_r1 + + + + + + SRS25726175 + SAMN49879669 + GSM9097131 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604774 + GSM9097130_r1 + + GSM9097130: Sample 4 5xFAD, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726174 + GSM9097130 + + + + GSM9097130 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726174 + SAMN49879670 + GSM9097130 + + Sample 4 5xFAD, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726174 + SAMN49879670 + GSM9097130 + + + + + + + SRR34444224 + GSM9097130_r1 + + + + GSM9097130_r1 + + + + + + SRS25726174 + SAMN49879670 + GSM9097130 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604773 + GSM9097129_r1 + + GSM9097129: Sample 3 5xFAD, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726173 + GSM9097129 + + + + GSM9097129 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726173 + SAMN49879671 + GSM9097129 + + Sample 3 5xFAD, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + 5xFAD + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726173 + SAMN49879671 + GSM9097129 + + + + + + + SRR34444225 + GSM9097129_r1 + + + + GSM9097129_r1 + + + + + + SRS25726173 + SAMN49879671 + GSM9097129 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604772 + GSM9097128_r1 + + GSM9097128: Sample 2 Control, Ventral, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726172 + GSM9097128 + + + + GSM9097128 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + NextSeq 2000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726172 + SAMN49879672 + GSM9097128 + + Sample 2 Control, Ventral, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + ventral part of the hippocampus + + + tissue + ventral part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726172 + SAMN49879672 + GSM9097128 + + + + + + + SRR34444226 + GSM9097128_r1 + + + + GSM9097128_r1 + + + + + + SRS25726172 + SAMN49879672 + GSM9097128 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + SRX29604771 + GSM9097127_r1 + + GSM9097127: Sample 1 Control, Dorsal, 8 month; Mus musculus; RNA-Seq + + + SRP599615 + GSE302153 + + + + + + + SRS25726171 + GSM9097127 + + + + GSM9097127 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.). snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample. + + + + + Illumina NovaSeq 6000 + + + + + + SRA2167374 + SUB15448143 + + + + Centre for Strategic Planning of FMBA of Russia + +
+ Pogodinskaya Street, 10, bld. 1 + Moscow + Russia +
+ + Vasiliy + Akimov + + + + + + SRP599615 + PRJNA1289087 + GSE302153 + + + Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer's Disease + + We performed snRNA-seq of 8, 16 and 22 month old mice of 5xFAD (B6SJL/Tg) line together with control B6SJL mice to assess the changes which occur due to progression of Alzheimer's disease. Overall design: Tissues of the dorsal and ventral parts of the hippocampi from 16 male animals of 8, 16 and 22 month old, respectively, were isolated to perform snRNA-seq. + GSE302153 + + + + + SRS25726171 + SAMN49879673 + GSM9097127 + + Sample 1 Control, Dorsal, 8 month + + 10090 + Mus musculus + + + + + bioproject + 1289087 + + + + + + + source_name + dorsal part of the hippocampus + + + tissue + dorsal part of the hippocampus + + + cell type + Hippocampal cells + + + age + 8 month old + + + Sex + male + + + genotype + Wild type + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS25726171 + SAMN49879673 + GSM9097127 + + + + + + + SRR34444227 + GSM9097127_r1 + + + + GSM9097127_r1 + + + + + + SRS25726171 + SAMN49879673 + GSM9097127 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/SRX26261721.runinfo b/tests/data/SRX26261721.runinfo new file mode 100644 index 0000000..d97e1ed --- /dev/null +++ b/tests/data/SRX26261721.runinfo @@ -0,0 +1,3 @@ +Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash +SRR30863712,2025-03-17 22:16:38,2024-10-02 12:42:46,182659799,25207052262,0,138,7564,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR030/30863/SRR30863712/SRR30863712.lite.1,SRX26261721,GSM8551336,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP536245,PRJNA1168106,4,1168106,SRS22801004,SAMN44025212,simple,9606,Homo sapiens,GSM8551336,,,,,,,no,,,,,"DEPARTMENT OF NEUROSCIENCE, THE OHIO STATE UNIVERSITY WEXNER MEDICAL CENTER",SRA1984609,,public,D4ADBA488EB92C43B001D58FE26A0AB2,421E99D08099DED1D7DC33A5925AF1EB +SRR30863713,2025-03-17 22:16:38,2024-10-02 12:44:28,183184846,25279508748,0,138,7581,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR030/30863/SRR30863713/SRR30863713.lite.1,SRX26261721,GSM8551336,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP536245,PRJNA1168106,4,1168106,SRS22801004,SAMN44025212,simple,9606,Homo sapiens,GSM8551336,,,,,,,no,,,,,"DEPARTMENT OF NEUROSCIENCE, THE OHIO STATE UNIVERSITY WEXNER MEDICAL CENTER",SRA1984609,,public,823BBC780F41C8CDBA7F6CFE9AC43D02,370716BA73FD3A2FFFF67D3F94A9DD5F diff --git a/tests/data/SRX26261721.xml b/tests/data/SRX26261721.xml new file mode 100644 index 0000000..ca10879 --- /dev/null +++ b/tests/data/SRX26261721.xml @@ -0,0 +1,308 @@ + + + + + + SRX26261721 + GSM8551336_r1 + + GSM8551336: HNO, D72, WT, Bio Rep 1; Homo sapiens; RNA-Seq + + + SRP536245 + GSE278619 + + + + + + + SRS22801004 + GSM8551336 + + + + GSM8551336 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + On Day 70 and Day 120, ten healthy HNOs of similar size were selected from each line. Five HNOs were combined to form a technical replicate. Each replicate was gently dissociated following the Single Cell Preparation Guide established by 10x Genomics. Approximately 10,000 live cells were used to generate scRNA-seq libraries with the 10x Chromium single-cell 3′ V2 library kit (10x Genomics) according to the manufacturer's instructions and paired-end sequencing was performed with a NovaSeq600 S2 flow cell using an Illumina NovaSeq 600 sequencer. + + + + + Illumina NovaSeq 6000 + + + + + + SRA1984609 + SUB14767101 + + + + Department of Neuroscience, The Ohio State University Wexner Medical Center + +
+ 616 Biomedical Research Tower, 460 W. 12th Ave + Columbus + OH + USA +
+ + Hongjun + Fu + + + + + + SRP536245 + PRJNA1168106 + GSE278619 + + + GRAMD1B is a novel regulator of lipid homeostasis, autophagic flux, and phosphorylated tau. + + Lipid dyshomeostasis and tau pathology are found in frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD). However, the relationship between lipid dyshomeostasis and tau pathology and molecular mechanisms underlying this relationship remain unclear. Using single-cell RNA-sequencing, we report that GRAM Domain Containing 1B (GRAMD1B), a nonvesicular cholesterol transporter, is increased in excitatory neurons of human neural organoids from patient-derived induced pluripotent stem cells with the MAPT R406W mutation compared to isogenic controls. Mutant neural organoids also exhibit altered lipid species, increased phosphorylated tau, and decreased neuronal activity. Increased GRAMD1B is also found in human FTLD and AD cases and PS19 tau mice. Phosphorylated tau, free cholesterol, and lipid droplets are also increased in human FTLD and AD cases. Furthermore, GRAMD1B overexpression increases pathological tau and lipid dyshomeostasis, which may be due to blocking of autophagic flux. Our findings suggest GRAMD1B may be a new player in the regulation of autophagic flux, cholesterol transport, and tau pathology in FTLD and AD. Overall design: Human iPSC lines were requested from the Tau consortium including iPSC F11362.11C11(WT: CRISPR-Cas9 edited isogenic control), iPSC F11362.11F10 (HET: MAPT R406W/R406R heterozygous), and iPSC GIH-143 (HOM: MAPT R406W/R406W homozygous). Human neural organoids (HNOs) were formed according to previously published protocols. On Day 70 and Day 120, ten healthy HNOs of similar size were selected from each line. Five HNOs were combined to form a technical replicate. Each replicate was gently dissociated following the Single Cell Preparation Guide established by 10x genomics. + GSE278619 + + + + + pubmed + 40204713 + + + + + + + SRS22801004 + SAMN44025212 + GSM8551336 + + HNO, D72, WT, Bio Rep 1 + + 9606 + Homo sapiens + + + + + bioproject + 1168106 + + + + + + + source_name + Human iPSC derived neural organoids (HNOs) + + + tissue + Human iPSC derived neural organoids (HNOs) + + + cell line + iPSC F11362.11C11 + + + genotype + WT: CRISPR-Cas9 edited isogenic control + + + technical replication + 5 HNOs pooled per library + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS22801004 + SAMN44025212 + GSM8551336 + + + + + + + SRR30863712 + GSM8551336_r1 + + + + GSM8551336_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTTB --read1PairFiles=S1_L001_I1_001.fastq.gz --read2PairFiles=S1_L001_I2_001.fastq.gz --read3PairFiles=S1_L001_R1_001.fastq.gz --read4PairFiles=S1_L001_R2_001.fastq.gz + + + + + + SRS22801004 + SAMN44025212 + GSM8551336 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + SRR30863713 + GSM8551336_r2 + + + + GSM8551336_r1 + + + + + loader + fastq-load.py + + + options + --readTypes=TTTB --read1PairFiles=S1_L002_I1_001.fastq.gz --read2PairFiles=S1_L002_I2_001.fastq.gz --read3PairFiles=S1_L002_R1_001.fastq.gz --read4PairFiles=S1_L002_R2_001.fastq.gz + + + + + + SRS22801004 + SAMN44025212 + GSM8551336 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/test_arrayexpress.py b/tests/test_arrayexpress.py new file mode 100644 index 0000000..2f1aaec --- /dev/null +++ b/tests/test_arrayexpress.py @@ -0,0 +1,6 @@ +from rnaseq_pipeline.sources.arrayexpress import DownloadArrayExpressExperiment + +def test(): + task = DownloadArrayExpressExperiment(experiment_id='E-MTAB-13839') + for download_sample_task in task.run(): + print(download_sample_task) \ No newline at end of file diff --git a/tests/test_miniml_utils.py b/tests/test_miniml_utils.py index 082073c..ce6e99b 100644 --- a/tests/test_miniml_utils.py +++ b/tests/test_miniml_utils.py @@ -1,9 +1,13 @@ +from os.path import join, dirname + from rnaseq_pipeline.miniml_utils import * +test_data_dir = join(dirname(__file__), 'data') + def test_collect_geo_samples(): - collect_geo_samples('tests/data/GSE100007_family.xml') - collect_geo_samples('tests/data/GSM69846.xml') + collect_geo_samples(join(test_data_dir, 'GSE100007_family.xml')) + collect_geo_samples(join(test_data_dir, 'GSM69846.xml')) def test_collect_geo_samples_info(): - collect_geo_samples_info('tests/data/GSE100007_family.xml') - collect_geo_samples_info('tests/data/GSM69846.xml') + collect_geo_samples_info(join(test_data_dir, 'GSE100007_family.xml')) + collect_geo_samples_info(join(test_data_dir, 'GSM69846.xml')) diff --git a/tests/test_rnaseq_utils.py b/tests/test_rnaseq_utils.py new file mode 100644 index 0000000..3d4134b --- /dev/null +++ b/tests/test_rnaseq_utils.py @@ -0,0 +1,9 @@ +from rnaseq_pipeline.rnaseq_utils import detect_common_fastq_name, SequencingFileType + +R1, R2 = SequencingFileType.R1, SequencingFileType.R2 + +def test_detect_simple_fastq_name(): + assert detect_common_fastq_name('123', ['3543_OF1B_5-2-D6-F3-R1.fq', '3543_OF1B_5-2-D6-F3-R2.fq']) == [R1, R2] + +def test_detect_name_with_lowercase(): + assert detect_common_fastq_name('SRR27810032', ['HLA00801R-I19.r1.fq.gz', 'HLA00801R-I19.r2.fq.gz']) == [R1, R2] diff --git a/tests/test_sra.py b/tests/test_sra.py index 4efde06..71a59d3 100644 --- a/tests/test_sra.py +++ b/tests/test_sra.py @@ -1,36 +1,266 @@ -import os -import shutil -from os.path import dirname +from os.path import join, dirname +from xml.etree import ElementTree -import luigi import pytest -from rnaseq_pipeline.sources.sra import DownloadSraExperimentRunInfo, DownloadSraProjectRunInfo, EmptyRunInfoError, \ - DownloadSraExperiment +from rnaseq_pipeline.sources.sra import DownloadSraExperimentMetadata, DownloadSraProjectRunInfo, read_xml_metadata, \ + SequencingFileType, DownloadSraExperiment, read_runinfo + +test_data_dir = join(dirname(__file__), 'data') + +I1, I2, R1, R2 = SequencingFileType.I1, SequencingFileType.I2, SequencingFileType.R1, SequencingFileType.R2 +R3 = SequencingFileType.R3 +R4 = SequencingFileType.R4 + +single_cell_datasets = ['GSE274829', + 'GSE302153', + 'GSE247070', + 'GSE297721', + 'GSE297666', + 'GSE296027', + 'GSE295459', + 'GSE283187', + 'GSE272344', + 'GSE272062', + 'GSE263191', + 'GSE247963', + 'GSE268343', + 'GSE249268', + 'GSE279548', + 'GSE261494', + 'GSE280296', + 'GSE261596', + 'GSE267764', + 'GSE287769', + 'GSE163314', + 'GSE254044', + 'GSE214244', + 'GSE202704', + 'GSE181989', + 'GSE218316', + 'GSE196929', + 'GSE198891', + 'GSE174667', + 'GSE212527', + 'GSE141784', + 'GSE247695', + 'GSE233276', + 'GSE232309', + 'GSE212505', + 'GSE179135', + 'GSE264408', + 'GSE283268', + 'GSE242271', + 'GSE205049', + 'GSE255460', + 'GSE184506', + 'GSE222510', + 'GSE222647', + 'GSE268642', + 'GSE173242', + 'GSE241349', + 'GSE284797', + 'GSE180672', + 'GSE240687', + 'GSE234421', + 'GSE234419', + 'GSE226822', + 'GSE226072', + 'GSE216766', + 'GSE213364', + 'GSE212351', + 'GSE157985', + 'GSE219280', + 'GSE263392', + 'GSE266033', + 'GSE275205', + 'GSE254104', + 'GSE235193', + 'GSE230451', + 'GSE234278', + 'GSE245339', + 'GSE235490', + 'GSE227515', + 'GSE212576', + 'GSE269499', + 'GSE218572', + 'GSE237816'] + +@pytest.fixture(params=single_cell_datasets) +def single_cell_datasets_fixture(request): + return request.param + +def test_read_xml_metadata(single_cell_datasets_fixture): + dataset = single_cell_datasets_fixture + meta = read_xml_metadata(join(test_data_dir, dataset + '.xml')) + assert len(meta) > 0 + common_layout = {} + + for run in meta: + # make sure that all runs within an experiment share the same layout + if run.srx not in common_layout: + common_layout[run.srx] = run.layout + # the order does not matter + assert set(run.layout) == set(common_layout[run.srx]) + +def test_read_xml_metadata_GSE247070(): + meta = read_xml_metadata(join(test_data_dir, 'GSE247070.xml')) + for run in meta: + if run.srx in ['SRR26686276' + 'SRR26686277' + 'SRR26686278' + 'SRR26686279' + 'SRR26686280' + 'SRR26686281' + 'SRR26686282' + 'SRR26686283' + 'SRR26686284' + 'SRR26686285' + 'SRR26686286' + 'SRR26686287' + 'SRR26686288' + 'SRR26686289' + 'SRR26686290' + 'SRR26686291']: + assert run.layout == [I1, R1, R2] + if run.srx in ['SRR26686292', + 'SRR26686293', + 'SRR26686294', + 'SRR26686295', + 'SRR26686296', + 'SRR26686297', + 'SRR26686298', + 'SRR26686299', + 'SRR26686300', + 'SRR26686301', + 'SRR26686302', + 'SRR26686303', + 'SRR26686304', + 'SRR26686305', + 'SRR26686306', + 'SRR26686307']: + assert run.layout == [R1, R2, I1, I2] + +def test_read_xml_metadata_GSE297721(): + """ + This is a typical case where I1 and I2 are the same size and thus impossible to tell apart if the inputs to + fastq-load.py are lacking. When that happens, we want to assume that the layout is I1, I2, R1, R2. + """ + meta = read_xml_metadata(join(test_data_dir, 'GSE297721.xml')) + for run in meta: + assert run.layout == [I1, I2, R1, R2] + +def test_read_xml_metadata_GSE274763(): + """This is an example where indices were in a separate run than the reads.""" + meta = read_xml_metadata(join(test_data_dir, 'GSE274763.xml')) + for run in meta: + # these are the problematic runs + if run.srx in ('SRX25689947', 'SRX25689948', 'SRX25689949', 'SRX25689950', 'SRX25689951', 'SRX25689952', + 'SRX25689953', 'SRX25689954'): + continue + if not run.layout == [R1, R2, I1, I2]: + print(run.srx) + +def test_read_xml_metadata_GSE181021(): + """This dataset is identified as paired-end, but only has one read file (which is a BAM).""" + # TODO: also GSE267933 GSE217511, GSE178257 and GSE253640 + meta = read_xml_metadata(join(test_data_dir, 'GSE181021.xml')) + for run in meta: + assert run.layout == [R1] + +def test_read_xml_metadata_GSE283187(): + """This dataset has a sample with 3 reads (R1, R2, R3) and an index (I1).""" + meta = read_xml_metadata(join(test_data_dir, 'GSE283187.xml')) + for run in meta: + print(run.srr) + if run.srr == 'SRR31555331': + assert run.layout == [I1, R1, I2, R2] + else: + assert run.layout == [I1, R1, R2] + +def test_read_xml_metadata_GSE174332(): + """In this dataset, the files passed to fastq-load.py were compressed.""" + meta = read_xml_metadata(join(test_data_dir, 'GSE174332.xml')) + for run in meta: + print(run.srr) + if run.srr == 'SRR14511669': + assert run.layout == [I1, R1, R2] + else: + assert run.layout == [R1, R2, I1] + +def test_read_xml_metadata_GSE104493(): + """This dataset has I1 reads with zero length""" + meta = read_xml_metadata(join(test_data_dir, 'GSE104493.xml')) + for run in meta: + print(run.srr) + assert run.layout == [I1, R1] + assert run.average_read_lengths[0] == 0.0 + +def test_read_xml_metadata_GSE125536(): + """This dataset does not have SRAFile entries, but it has fastq-load.py inputs which can be used as a fallback.""" + meta = read_xml_metadata(join(test_data_dir, 'GSE125536.xml')) + for run in meta: + assert run.layout == [R1, R2, R3, R4] + +def test_read_xml_metadata_GSE128117(): + """This dataset has a sample with 3 reads (R1, R2, R3) and an index (I1).""" + meta = read_xml_metadata(join(test_data_dir, 'GSE128117.xml')) + for run in meta: + print(run.srr) + assert run.layout == [R1, I1] + +def test_read_xml_metadata_SRX26261721(): + meta = read_xml_metadata(join(test_data_dir, 'SRX26261721.xml')) + assert len(meta) == 2 + assert meta[0].srx == 'SRX26261721' + assert meta[0].srr == 'SRR30863712' + assert meta[0].is_paired + assert meta[0].fastq_filenames == ['S1_L001_I1_001.fastq.gz', + 'S1_L001_I2_001.fastq.gz', + 'S1_L001_R1_001.fastq.gz', + 'S1_L001_R2_001.fastq.gz'] + assert meta[0].layout == [SequencingFileType.I1, SequencingFileType.I2, SequencingFileType.R1, + SequencingFileType.R2] + + assert meta[1].srx == 'SRX26261721' + assert meta[1].srr == 'SRR30863713' + assert meta[1].is_paired + assert meta[1].fastq_filenames == ['S1_L002_I1_001.fastq.gz', + 'S1_L002_I2_001.fastq.gz', + 'S1_L002_R1_001.fastq.gz', + 'S1_L002_R2_001.fastq.gz'] + assert meta[1].layout == [SequencingFileType.I1, SequencingFileType.I2, SequencingFileType.R1, + SequencingFileType.R2] + +def test_read_runinfo(): + meta = read_runinfo(join(test_data_dir, 'SRX26261721.runinfo')) + assert len(meta) == 2 + assert len(meta.columns) == 47 + assert meta.Run.tolist() == ['SRR30863712', 'SRR30863713'] + +def test_read_runinfo_no_header(): + meta = read_runinfo(join(test_data_dir, 'SRX12752257.runinfo')) + assert len(meta) == 1 + assert len(meta.columns) == 47 + assert meta.Run.tolist() == ['SRR16550084'] + +def test_download_single_cell(): + task = DownloadSraExperimentMetadata(srx='SRX26261721') + task.run() + tree = ElementTree.parse(task.output().path) + task2 = DownloadSraExperiment(srx='SRX26261721') + task2.run() + for run in task2.output(): + assert len(run.files) == 4 + assert run.layout == ('I1', 'I2', 'R1', 'R2') def test_download_sra_experiment_run_info(): - task = DownloadSraExperimentRunInfo(srx='SRX12752257') + task = DownloadSraExperimentMetadata(srx='SRX12752257') task.run() contents = task.output().open('r').read() assert contents assert task.complete() -def test_empty_sra_file_raises_exception(): - fake_sra_accession = 'SRX129093021' - task = DownloadSraExperimentRunInfo(srx=fake_sra_accession) - with pytest.raises(EmptyRunInfoError, match=fake_sra_accession): - task.run() - assert not task.output().exists() - assert not task.complete() - -def test_sra_file_with_missing_header(): - download_runinfo_task = DownloadSraExperimentRunInfo(srx='SRX12752257') - download_runinfo_task.output() - os.makedirs(dirname(download_runinfo_task.output().path), exist_ok=True) - shutil.copy('tests/data/SRX12752257.runinfo', download_runinfo_task.output().path) - assert download_runinfo_task.complete() - assert luigi.build([DownloadSraExperiment(srx='SRX12752257')], local_scheduler=True) - def test_download_sra_project_run_info(): task = DownloadSraProjectRunInfo(srp='SRP342859') task.run() diff --git a/tests/test_tasks.py b/tests/test_tasks.py index 7a04417..7b41fd1 100644 --- a/tests/test_tasks.py +++ b/tests/test_tasks.py @@ -1,6 +1,6 @@ import pytest -from gemma import GemmaTaskMixin +from rnaseq_pipeline.gemma import GemmaTaskMixin from rnaseq_pipeline.sources.geo import match_geo_platform from rnaseq_pipeline.tasks import * diff --git a/tests/test_webviewer.py b/tests/test_webviewer.py index 62e2b5f..0c980f5 100644 --- a/tests/test_webviewer.py +++ b/tests/test_webviewer.py @@ -11,6 +11,7 @@ def test_experiment_summary(client): res = client.get('/experiment/GSE87750') assert res.status == '200 OK' +@pytest.mark.skip() def test_experiment_batch_info(client): res = client.get('/experiment/GSE87750/batch-info') assert res.status == '200 OK' From 749eea6bdbd2037a4a851f9a11b386294809eaea Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 23 Sep 2025 16:01:17 -0700 Subject: [PATCH 06/45] Ignore SRA runs that do not contain transcriptomic RNA-Seq data --- rnaseq_pipeline/sources/sra.py | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index b193210..da38089 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -80,6 +80,7 @@ class SraRunMetadata: def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: """ + Extract transcriptomic RNA-Seq runs from the given SRA XML metadata file. :param path: Path to the XML file containing SRA run metadata. :param include_invalid_runs: If True, include runs that do not have any suitable metadata that can be used to determine the layout. @@ -92,6 +93,20 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr = run.attrib['accession'] srx = run.find('EXPERIMENT_REF').attrib['accession'] + + library_strategy = root.find( + 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY') + library_source = root.find( + 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE') + + if library_strategy is not None and library_strategy.text not in ['RNA-Seq']: + logger.warning('%s Ignoring run with %s library strategy.', srr, library_strategy.text) + continue + + if library_source is not None and library_source.text not in ['TRANSCRIPTOMIC', 'TRANSCRIPTOMIC SINGLE CELL']: + logger.warning('%s: Ignoring run with %s library source.', srr, library_source.text) + continue + is_single_end = root.find( 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/SINGLE') is not None is_paired = root.find( @@ -389,7 +404,7 @@ def run(self): meta = [r for r in meta if r.srr in self.srr] if not meta: - raise ValueError(f'No SRA runs found for {self.srx}.') + raise ValueError(f'No valid SRA runs found for {self.srx}. Valid runs must be transcriptomic RNA-Seq.') metadata = dict(self.metadata) # do not override the sample_id when invoked from DownloadGeoSample or DownloadGemmaExperiment From 1d0932d0c849add4d577c18bbff651b882f56e1a Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 23 Sep 2025 16:06:51 -0700 Subject: [PATCH 07/45] Parse the --readTypes option Add more metadata. --- rnaseq_pipeline/sources/sra.py | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index da38089..2547b23 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -68,9 +68,11 @@ class SraRunMetadata: """A digested SRA run metadata""" srx: str srr: str + is_single_end: bool is_paired: bool - fastq_filenames: list[str] - fastq_file_sizes: list[int] + fastq_filenames: Optional[list[str]] + fastq_file_sizes: Optional[list[int]] + fastq_file_types: Optional[list[str]] # only available if statistics were present in the XML metadata number_of_spots: Optional[int] average_read_lengths: Optional[list[float]] @@ -134,8 +136,11 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: if loader == 'fastq-load.py': # parse options... # TODO: use argparse or something safer + fastq_load_read_types = None fastq_load_files = [] if options: + if '--readTypes' in options and options['--readTypes'] is not None: + fastq_load_read_types = list(str(options['--readTypes'])) opts = ['--read1PairFiles', '--read2PairFiles', '--read3PairFiles', @@ -149,6 +154,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: issues |= SraRunIssue.NO_FASTQ_LOAD_OPTIONS else: issues |= SraRunIssue.NO_FASTQ_LOAD + fastq_load_read_types = None fastq_load_files = None statistics = run.find('Statistics') @@ -173,6 +179,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: sra_files = sorted(sra_files, key=lambda f: fastq_load_files.index(f.attrib['filename'])) fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + fastq_file_types = fastq_load_read_types # try to add a .gz suffix to the SRA files elif set(fastq_load_files) == set([sf.attrib['filename'] + '.gz' for sf in sra_files]): @@ -183,6 +190,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: key=lambda f: fastq_load_files.index(f.attrib['filename'] + '.gz')) fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + fastq_file_types = fastq_load_read_types elif sra_files: logging.warning( @@ -193,6 +201,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_files) fastq_filenames = fastq_load_files fastq_file_sizes = None + fastq_file_types = fastq_load_read_types issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS else: @@ -201,6 +210,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, options, fastq_load_files) fastq_filenames = fastq_load_files fastq_file_sizes = None + fastq_file_types = fastq_load_read_types # use spot statistics to determine the order of the files by matching their sizes with the sizes of the files # this is less reliable than using the fastq-load.py options, but it is still better than nothing @@ -223,6 +233,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: enumerate(sra_files)] fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + fastq_file_types = None else: # shot logger.warning( @@ -230,6 +241,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, len(reads_by_size), len(files_by_size)) fastq_filenames = None fastq_file_sizes = None + fastq_file_types = None issues |= SraRunIssue.MISMATCHED_READ_SIZES else: # this is extremely common, so it's not worth warning about it @@ -238,6 +250,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, read_sizes) fastq_filenames = None fastq_file_sizes = None + fastq_file_types = None issues |= SraRunIssue.AMBIGUOUS_READ_SIZES else: @@ -249,9 +262,11 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] result.append(SraRunMetadata(srx, srr, + is_single_end=is_single_end, is_paired=is_paired, fastq_filenames=fastq_filenames, fastq_file_sizes=fastq_file_sizes, + fastq_file_types=None, number_of_spots=None, average_read_lengths=None, fastq_load_options=None, @@ -270,9 +285,11 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: continue result.append(SraRunMetadata(srx, srr, + is_single_end=is_single_end, is_paired=is_paired, fastq_filenames=fastq_filenames, fastq_file_sizes=fastq_file_sizes, + fastq_file_types=fastq_file_types, number_of_spots=number_of_spots, average_read_lengths=spot_read_lengths, fastq_load_options=options if loader == 'fastq-load.py' else None, From bb119828c158bf7f38810d35b06e417c7806c324 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Wed, 24 Sep 2025 11:08:58 -0700 Subject: [PATCH 08/45] Improve and fix logging for extracting SRA metadata Rename fastq_file_types to read_types and add an enumerated type for possible values. --- rnaseq_pipeline/rnaseq_utils.py | 8 +-- rnaseq_pipeline/sources/sra.py | 93 ++++++++++++++++++++------------- 2 files changed, 60 insertions(+), 41 deletions(-) diff --git a/rnaseq_pipeline/rnaseq_utils.py b/rnaseq_pipeline/rnaseq_utils.py index d9575a3..27b3618 100644 --- a/rnaseq_pipeline/rnaseq_utils.py +++ b/rnaseq_pipeline/rnaseq_utils.py @@ -36,17 +36,17 @@ def detect_layout(run_id: str, filenames: Optional[list[str]], if filenames: if layout := detect_bcl2fastq_name(run_id, filenames): logger.info('%s: Inferred file types: %s from file names conforming to bcl2fastq output: %s.', run_id, - layout, filenames) + '|'.join(l.name for l in layout), ', '.join(filenames)) return layout if layout := detect_common_fastq_name(run_id, filenames): - logger.info('%s: Inferred file types: %s from file names conforming to a common output.', run_id, - layout, filenames) + logger.info('%s: Inferred file types: %s from file names conforming to a common output: %s.', run_id, + '|'.join(l.name for l in layout), ', '.join(filenames)) return layout if layout := detect_fallback_fastq_name(run_id, filenames): logger.warning('%s: Inferred file types: %s from file names with fallback name patterns: %s. This is highly inaccurate.', - run_id, layout, filenames) + run_id, '|'.join(l.name for l in layout), ', '.join(filenames)) return layout number_of_files = len(filenames) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 2547b23..50970ad 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -63,6 +63,13 @@ class SraRunIssue(enum.IntFlag): MISMATCHED_READ_SIZES = enum.auto() INVALID_RUN = enum.auto() +class SraReadType(enum.Enum): + """ + Type of read in a spot. + """ + TECHNICAL = 'T' + BIOLOGICAL = 'B' + @dataclass class SraRunMetadata: """A digested SRA run metadata""" @@ -72,7 +79,9 @@ class SraRunMetadata: is_paired: bool fastq_filenames: Optional[list[str]] fastq_file_sizes: Optional[list[int]] - fastq_file_types: Optional[list[str]] + # currently only available if --readTypes options were passed to the fastq-load.py loader, I'd like to know if this + # is stored elsewhere though, because I can see it in the UI. + read_types: Optional[list[SraReadType]] # only available if statistics were present in the XML metadata number_of_spots: Optional[int] average_read_lengths: Optional[list[float]] @@ -140,7 +149,8 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_files = [] if options: if '--readTypes' in options and options['--readTypes'] is not None: - fastq_load_read_types = list(str(options['--readTypes'])) + fastq_load_read_types = [SraReadType.BIOLOGICAL if rt == 'B' else SraReadType.TECHNICAL for rt in + str(options['--readTypes'])] opts = ['--read1PairFiles', '--read2PairFiles', '--read3PairFiles', @@ -158,7 +168,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_files = None statistics = run.find('Statistics') - if statistics: + if statistics is not None: number_of_spots = int(statistics.attrib['nreads']) reads = sorted(statistics.findall('Read'), key=lambda r: int(r.attrib['index'])) spot_read_lengths = [float(r.attrib['average']) for r in reads] @@ -179,70 +189,79 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: sra_files = sorted(sra_files, key=lambda f: fastq_load_files.index(f.attrib['filename'])) fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] - fastq_file_types = fastq_load_read_types + read_types = fastq_load_read_types # try to add a .gz suffix to the SRA files elif set(fastq_load_files) == set([sf.attrib['filename'] + '.gz' for sf in sra_files]): logger.warning( '%s: The SRA files lack .gz extensions: %s, but still correspond to fastq-load.py options: %s, will use those to reorder the SRA files.', - srx, [sf.attrib['filename'] for sf in sra_files], fastq_load_files) + srx, ', '.join(sf.attrib['filename'] for sf in sra_files), ', '.join(fastq_load_files)) sra_files = sorted(sra_files, key=lambda f: fastq_load_files.index(f.attrib['filename'] + '.gz')) fastq_filenames = [sf.attrib['filename'] for sf in sra_files] fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] - fastq_file_types = fastq_load_read_types + read_types = fastq_load_read_types elif sra_files: logging.warning( "%s: The SRA files: %s do not match arguments passed to fastq-load.py: %s. The filenames passed to fastq-load.py will be used instead: %s.", srr, - [sf.attrib['filename'] for sf in sra_files], - options, + ', '.join(sf.attrib['filename'] for sf in sra_files), + ' '.join(k + '=' + v if v else 'k' for k, v in options.items()), fastq_load_files) fastq_filenames = fastq_load_files fastq_file_sizes = None - fastq_file_types = fastq_load_read_types + read_types = fastq_load_read_types issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS else: logging.warning( "%s: No SRA files found, but the arguments of fastq-load.py are present: %s. The filenames passed to fastq-load.py will be used: %s.", - srr, options, fastq_load_files) + srr, ' '.join(k + '=' + v if v else 'k' for k, v in options.items()), ', '.join(fastq_load_files)) fastq_filenames = fastq_load_files fastq_file_sizes = None - fastq_file_types = fastq_load_read_types + read_types = fastq_load_read_types # use spot statistics to determine the order of the files by matching their sizes with the sizes of the files # this is less reliable than using the fastq-load.py options, but it is still better than nothing # we can only use this strategy if all the read sizes are different and can be related to the file sizes - elif statistics: + elif statistics is not None: # check if the sizes are unambiguous? read_sizes = [int(read.attrib['count']) * float(read.attrib['average']) for read in reads] if len(set(read_sizes)) == len(read_sizes): - # sort the files according to the layout - # sort the layout according to the average read size - reads_by_size = [e[0] for e in sorted(enumerate(reads), - key=lambda e: int(e[1].attrib['count']) * float( - e[1].attrib['average']))] - files_by_size = [e[0] for e in sorted(enumerate(sra_files), key=lambda e: int(e[1].attrib['size']))] - - if len(reads_by_size) == len(files_by_size): - if reads_by_size != files_by_size: - logger.info('%s: Reordering SRA files to match the read sizes in the spot...', srr) - sra_files = [sra_files[reads_by_size.index(files_by_size[i])] for i, sra_file in - enumerate(sra_files)] - fastq_filenames = [sf.attrib['filename'] for sf in sra_files] - fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] - fastq_file_types = None + if sra_files: + # sort the files according to the layout + # sort the layout according to the average read size + reads_by_size = [e[0] for e in sorted(enumerate(reads), + key=lambda e: int(e[1].attrib['count']) * float( + e[1].attrib['average']))] + files_by_size = [e[0] for e in sorted(enumerate(sra_files), key=lambda e: int(e[1].attrib['size']))] + + if len(reads_by_size) == len(files_by_size): + if reads_by_size != files_by_size: + logger.info('%s: Reordering SRA files to match the read sizes in the spot...', srr) + sra_files = [sra_files[reads_by_size.index(files_by_size[i])] for i, sra_file in + enumerate(sra_files)] + fastq_filenames = [sf.attrib['filename'] for sf in sra_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + read_types = None + else: + logger.warning( + '%s: The number of reads: %d and files: %d do not correspond, cannot use them to order SRA files by filesize. Only the spot metadata will be used to determine the layout.', + srr, len(reads_by_size), len(files_by_size)) + fastq_filenames = None + fastq_file_sizes = None + read_types = None + issues |= SraRunIssue.MISMATCHED_READ_SIZES else: - # shot - logger.warning( - '%s: The number of reads: %d and files: %d do not correspond, cannot use them to order SRA files by filesize. Only the spot metadata will be used to determine the layout.', - srr, len(reads_by_size), len(files_by_size)) + # this is extremely common, so it's not worth warning about it + logger.info( + '%s: No SRA file to order. Only the spot metadata will be used to determine the layout.', + srr) fastq_filenames = None fastq_file_sizes = None - fastq_file_types = None - issues |= SraRunIssue.MISMATCHED_READ_SIZES + read_types = None + issues |= SraRunIssue.NO_SRA_FILES else: # this is extremely common, so it's not worth warning about it logger.info( @@ -250,12 +269,12 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, read_sizes) fastq_filenames = None fastq_file_sizes = None - fastq_file_types = None + read_types = None issues |= SraRunIssue.AMBIGUOUS_READ_SIZES else: issues |= SraRunIssue.INVALID_RUN - logger.warning( + logger.info( '%s: No information found that can be used to order SRA files, ignoring that run.', srr) if include_invalid_runs: @@ -266,7 +285,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: is_paired=is_paired, fastq_filenames=fastq_filenames, fastq_file_sizes=fastq_file_sizes, - fastq_file_types=None, + read_types=None, number_of_spots=None, average_read_lengths=None, fastq_load_options=None, @@ -289,7 +308,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: is_paired=is_paired, fastq_filenames=fastq_filenames, fastq_file_sizes=fastq_file_sizes, - fastq_file_types=fastq_file_types, + read_types=read_types, number_of_spots=number_of_spots, average_read_lengths=spot_read_lengths, fastq_load_options=options if loader == 'fastq-load.py' else None, From 7861dcc46908e9b3495dc4d3c07a8f1ebc8e114b Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Wed, 24 Sep 2025 11:18:02 -0700 Subject: [PATCH 09/45] Validate SRA metadata by reading it prior to writing it to disk --- rnaseq_pipeline/sources/sra.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 50970ad..bd74e39 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -402,8 +402,11 @@ class DownloadSraExperimentMetadata(TaskWithMetadataMixin, RerunnableTaskMixin, def run(self): if self.output().is_stale(): logger.info('%s is stale, redownloading...', self.output()) + meta = retrieve_sra_metadata(self.srx, format='xml') + # basic validation + ET.fromstring(meta) with self.output().open('w') as f: - f.write(retrieve_sra_metadata(self.srx, format='xml')) + f.write(meta) def output(self): return ExpirableLocalTarget(join(cfg.OUTPUT_DIR, cfg.METADATA, 'sra', '{}.xml'.format(self.srx)), From 0035f859a6e10ba9054872302a373d96f63117d9 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 25 Sep 2025 11:40:21 -0700 Subject: [PATCH 10/45] Do not open the browser in Google OAuth flow --- rnaseq_pipeline/gsheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rnaseq_pipeline/gsheet.py b/rnaseq_pipeline/gsheet.py index 16e2e88..e95b0d1 100644 --- a/rnaseq_pipeline/gsheet.py +++ b/rnaseq_pipeline/gsheet.py @@ -33,7 +33,7 @@ def _authenticate(): else: flow = InstalledAppFlow.from_client_secrets_file( CREDENTIALS_FILE, SCOPES) - creds = flow.run_local_server(port=0) + creds = flow.run_local_server(open_browser=False, port=0) # Save the credentials for the next run with open(token_path, 'wb') as token: pickle.dump(creds, token) From 3e88020cf6511dd0f39dcfdb934feb660772ed99 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Sat, 4 Oct 2025 17:03:55 -0700 Subject: [PATCH 11/45] Add support for 10x BAM submissions to SRA Detect which pipeline branch to take by looking up the assay type of a dataset. Add a special case for FAC-sorted single-cell datasets that should be treated as bulk. Add support for 10x BAM SRA submissions. This is done by looking up the header of the BAM files to infer the sequencing layout and calling bamtofastq downstream on the original submission. Temporarily use the branch of bioluigi with improved sratools support and Cell Ranger. --- environment.yml | 2 + example.luigi.cfg | 2 + rnaseq_pipeline/gemma.py | 64 +++++- rnaseq_pipeline/miniml_utils.py | 4 +- rnaseq_pipeline/platforms.py | 5 +- rnaseq_pipeline/rnaseq_utils.py | 5 +- rnaseq_pipeline/sources/gemma.py | 43 +--- rnaseq_pipeline/sources/geo.py | 21 +- rnaseq_pipeline/sources/local.py | 4 +- rnaseq_pipeline/sources/sra.py | 240 +++++++++++++++++---- rnaseq_pipeline/tasks.py | 360 ++++++++++++++++++------------- setup.py | 2 +- tests/test_gemma.py | 7 + tests/test_sra.py | 58 ++++- 14 files changed, 561 insertions(+), 256 deletions(-) diff --git a/environment.yml b/environment.yml index 0dbbd7c..94d8d6a 100644 --- a/environment.yml +++ b/environment.yml @@ -14,3 +14,5 @@ dependencies: - star==2.7.3a - entrez-direct - perl # rsem expects this +- samtools +- curl diff --git a/example.luigi.cfg b/example.luigi.cfg index 5cfa6ea..3316a03 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -61,6 +61,8 @@ SLACK_WEBHOOK_URL= # location where tools like prefetch and fastq-dump will store downloaded SRA files # you can get this value with vdb-config -p ncbi_public_dir=/cosmos/scratch/ncbi/public +samtools_bin=samtools +bamtofastq_bin=bamtofastq [rnaseq_pipeline.gemma] cli_bin=gemma-cli diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py index 16346f1..3465891 100644 --- a/rnaseq_pipeline/gemma.py +++ b/rnaseq_pipeline/gemma.py @@ -1,3 +1,5 @@ +import enum +import logging import os import subprocess from getpass import getpass @@ -8,6 +10,8 @@ from luigi.contrib.external_program import ExternalProgramTask from requests.auth import HTTPBasicAuth +logger = logging.getLogger(__name__) + class gemma(luigi.Config): task_namespace = 'rnaseq_pipeline' baseurl: str = luigi.Parameter() @@ -48,6 +52,9 @@ def _query_api(self, endpoint): def datasets(self, experiment_id): return self._query_api(join('datasets', experiment_id)) + def dataset_annotations(self, experiment_id): + return self._query_api(join('datasets', experiment_id, 'annotations')) + def dataset_has_batch(self, experiment_id): return self._query_api(join('datasets', experiment_id, 'hasbatch')) @@ -57,7 +64,7 @@ def samples(self, experiment_id): def platforms(self, experiment_id): return self._query_api(join('datasets', experiment_id, 'platforms')) -class GemmaTaskMixin: +class GemmaTaskMixin(luigi.Task): experiment_id = luigi.Parameter() def __init__(self, *kwargs, **kwds): @@ -101,9 +108,11 @@ def reference_id(self): except KeyError: raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) + @property def single_cell_reference_id(self): try: - return {'human': cfg.human_single_cell_reference_id, 'mouse': cfg.mouse_single_cell_reference_id, 'rat': cfg.rat_single_cell_reference_id}[ + return {'human': cfg.human_single_cell_reference_id, 'mouse': cfg.mouse_single_cell_reference_id, + 'rat': cfg.rat_single_cell_reference_id}[ self.taxon] except KeyError: raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) @@ -112,6 +121,57 @@ def single_cell_reference_id(self): def platform_short_name(self): return f'Generic_{self.taxon}_ncbiIds' + @property + def assay_type(self): + # Possible values: + # bulk RNA-seq assay http://purl.obolibrary.org/obo/OBI_0003090 11345 + # transcription profiling by array assay http://purl.obolibrary.org/obo/OBI_0001463 10788 + # transcription profiling by high throughput sequencing http://www.ebi.ac.uk/efo/EFO_0002770 262 + # single-cell RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0002631 248 + # single-nucleus RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0003109 150 + # transcription profiling by array http://www.ebi.ac.uk/efo/EFO_0002768 79 + # single-cell RNA sequencing http://www.ebi.ac.uk/efo/EFO_0008913 5 + # single nucleus RNA sequencing http://www.ebi.ac.uk/efo/EFO_0009809 4 + # fluorescence-activated cell sorting http://www.ebi.ac.uk/efo/EFO_0009108 2 + # RIP-seq http://www.ebi.ac.uk/efo/EFO_0005310 1 + # These were pulled from Gemma on October 1st, 2025 + + assay_type_class_uri = 'http://purl.obolibrary.org/obo/OBI_0000070' + microarray_uris = ['http://purl.obolibrary.org/obo/OBI_0001463', 'http://www.ebi.ac.uk/efo/EFO_0002768'] + bulk_rnaseq_uris = ['http://purl.obolibrary.org/obo/OBI_0003090'] + sc_rnaseq_uris = ['http://purl.obolibrary.org/obo/OBI_0002631', 'http://www.ebi.ac.uk/efo/EFO_0008913', + 'http://www.ebi.ac.uk/efo/EFO_0009809', 'http://purl.obolibrary.org/obo/OBI_0003109'] + fac_sorted_uri = 'http://www.ebi.ac.uk/efo/EFO_0009108' + + annotations = self._gemma_api.dataset_annotations(self.experiment_id) + fac_sorted = any(annotation['classUri'] == assay_type_class_uri and annotation['termUri'] == fac_sorted_uri + for annotation in annotations) + for annotation in annotations: + if annotation['classUri'] == assay_type_class_uri: + value_uri = annotation['termUri'] + if value_uri in microarray_uris: + return GemmaAssayType.MICROARRAY + elif value_uri in bulk_rnaseq_uris: + return GemmaAssayType.BULK_RNA_SEQ + elif value_uri in sc_rnaseq_uris: + if fac_sorted: + # fac-sorted scRNA-Seq is treated as bulk + logger.info('%s: Dataset is a FAC-sorted single-cell RNA-Seq, will treat as bulk RNA-Seq.', + self.dataset_short_name) + return GemmaAssayType.BULK_RNA_SEQ + else: + return GemmaAssayType.SINGLE_CELL_RNA_SEQ + + # assume bulk + logger.warning('%s: No suitable experiment tag to determine the assay type, will assume bulk RNA-Seq.', + self.dataset_short_name) + return GemmaAssayType.BULK_RNA_SEQ + +class GemmaAssayType(enum.Enum): + MICROARRAY = 0 + BULK_RNA_SEQ = 1 + SINGLE_CELL_RNA_SEQ = 2 + class GemmaCliTask(GemmaTaskMixin, ExternalProgramTask): """ Base class for tasks that wraps Gemma CLI. diff --git a/rnaseq_pipeline/miniml_utils.py b/rnaseq_pipeline/miniml_utils.py index fe0ccbb..2d4028f 100644 --- a/rnaseq_pipeline/miniml_utils.py +++ b/rnaseq_pipeline/miniml_utils.py @@ -36,9 +36,9 @@ def collect_geo_samples(f): continue if sample_type.text == 'SRA': library_source = x.find('miniml:Library-Source', ns) - if library_source is not None and library_source.text == 'transcriptomic': + if library_source is not None and library_source.text in ['transcriptomic', 'transcriptomic single cell']: library_strategy = x.find('miniml:Library-Strategy', ns) - if library_strategy is not None and library_strategy.text in ['RNA-Seq', 'ssRNA-seq', 'OTHER']: + if library_strategy is not None and library_strategy.text in ['RNA-Seq', 'ssRNA-seq', 'scRNA-Seq', 'snRNA-Seq', 'OTHER']: gsm_identifiers.add(gsm_id.text) return gsm_identifiers diff --git a/rnaseq_pipeline/platforms.py b/rnaseq_pipeline/platforms.py index 9c50339..462cc61 100644 --- a/rnaseq_pipeline/platforms.py +++ b/rnaseq_pipeline/platforms.py @@ -1,16 +1,19 @@ +from abc import abstractmethod, ABC from typing import Optional from bioluigi.tasks import cutadapt -class Platform: +class Platform(ABC): """ :param name: Platform common name """ name: Optional[str] = None + @abstractmethod def get_trim_single_end_reads_task(self, r1, dest, **kwargs): raise NotImplementedError + @abstractmethod def get_trim_paired_reads_task(self, r1, r2, r1_dest, r2_dest, **kwargs): raise NotImplementedError diff --git a/rnaseq_pipeline/rnaseq_utils.py b/rnaseq_pipeline/rnaseq_utils.py index 27b3618..2557bb6 100644 --- a/rnaseq_pipeline/rnaseq_utils.py +++ b/rnaseq_pipeline/rnaseq_utils.py @@ -20,6 +20,7 @@ class SequencingFileType(enum.Enum): def detect_layout(run_id: str, filenames: Optional[list[str]], file_sizes: Optional[list[int]] = None, average_read_lengths: Optional[list[float]] = None, + read_types: Optional[list[SequencingFileType]] = None, is_single_end: bool = False, is_paired: bool = False): """Detects the layout of the sequencing run files based on their names and various additional information. @@ -50,8 +51,10 @@ def detect_layout(run_id: str, filenames: Optional[list[str]], return layout number_of_files = len(filenames) - else: + elif average_read_lengths: number_of_files = len(average_read_lengths) + else: + number_of_files = len(read_types) # assume single-end read if only one file is present if number_of_files == 1: diff --git a/rnaseq_pipeline/sources/gemma.py b/rnaseq_pipeline/sources/gemma.py index daa43f3..5edaf3a 100644 --- a/rnaseq_pipeline/sources/gemma.py +++ b/rnaseq_pipeline/sources/gemma.py @@ -1,12 +1,8 @@ -import gzip import logging -import os -from os.path import join import luigi -from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask -from luigi.util import requires +from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask from .geo import DownloadGeoSample from .sra import DownloadSraExperiment from ..config import rnaseq_pipeline @@ -45,39 +41,4 @@ def run(self): else: logger.warning('Downloading %s from %s is not supported.', accession, external_database) continue - yield download_sample_tasks - -@requires(DownloadGemmaExperiment) -class ExtractGemmaExperimentBatchInfo(luigi.Task): - experiment_id: str - - def run(self): - with self.output().open('w') as info_out: - for sample in self.requires().requires(): - if not isinstance(sample, DownloadGeoSample): - logger.warning('Extracting batch info from %s is not supported.', sample) - continue - - if len(sample.output()) == 0: - logger.warning( - 'GEO sample %s has no associated FASTQs from which batch information can be extracted.', - sample.sample_id) - continue - - # TODO: find a cleaner way to obtain the SRA run accession - for fastq in sample.output(): - # strip the two extensions (.fastq.gz) - fastq_name, _ = os.path.splitext(fastq.path) - fastq_name, _ = os.path.splitext(fastq_name) - - fastq_id = os.path.basename(fastq_name) - - platform_id, srx_uri = sample_geo_metadata[sample.sample_id] - - with gzip.open(fastq.path, 'rt') as f: - fastq_header = f.readline().rstrip() - - info_out.write('\t'.join([sample.sample_id, fastq_id, platform_id, srx_uri, fastq_header]) + '\n') - - def output(self): - return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'fastq_headers', '{}.fastq-header'.format(self.experiment_id))) + yield download_sample_tasks \ No newline at end of file diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py index efb0c23..394c918 100644 --- a/rnaseq_pipeline/sources/geo.py +++ b/rnaseq_pipeline/sources/geo.py @@ -189,20 +189,21 @@ def run(self): continue # TODO: find a cleaner way to obtain the SRA run accession - for fastq in sample.output(): - # strip the two extensions (.fastq.gz) - fastq_name, _ = os.path.splitext(fastq.path) - fastq_name, _ = os.path.splitext(fastq_name) + for run in sample.output(): + for fastq in run.files: + # strip the two extensions (.fastq.gz) + fastq_name, _ = os.path.splitext(fastq) + fastq_name, _ = os.path.splitext(fastq_name) - # is this necessary? - fastq_id = os.path.basename(fastq_name) + # is this necessary? + fastq_id = os.path.basename(fastq_name) - platform_id, srx_uri = sample_geo_metadata[sample.sample_id] + platform_id, srx_uri = sample_geo_metadata[sample.sample_id] - with gzip.open(fastq.path, 'rt') as f: - fastq_header = f.readline().rstrip() + with gzip.open(fastq, 'rt') as f: + fastq_header = f.readline().rstrip() - info_out.write('\t'.join([sample.sample_id, fastq_id, platform_id, srx_uri, fastq_header]) + '\n') + info_out.write('\t'.join([sample.sample_id, fastq_id, platform_id, srx_uri, fastq_header]) + '\n') def output(self): # TODO: organize batch info per source diff --git a/rnaseq_pipeline/sources/local.py b/rnaseq_pipeline/sources/local.py index 63c7a83..20af2a6 100644 --- a/rnaseq_pipeline/sources/local.py +++ b/rnaseq_pipeline/sources/local.py @@ -31,5 +31,5 @@ class DownloadLocalExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): experiment_id: str = luigi.Parameter() def run(self): - yield [DownloadLocalSample(self.experiment_id, os.path.basename(f)) - for f in glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, '*'))] + for f in glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, '*')): + yield DownloadLocalSample(self.experiment_id, os.path.basename(f)) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index bd74e39..9bfad58 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -5,6 +5,7 @@ import gzip import logging import os +import re import subprocess import xml.etree.ElementTree as ET from dataclasses import dataclass @@ -14,10 +15,11 @@ import luigi import pandas as pd -from bioluigi.tasks import sratoolkit -from bioluigi.tasks.utils import TaskWithMetadataMixin, DynamicTaskWithOutputMixin, DynamicWrapperTask from luigi.util import requires +from bioluigi.scheduled_external_program import ScheduledExternalProgramTask +from bioluigi.tasks import sratoolkit +from bioluigi.tasks.utils import TaskWithMetadataMixin, DynamicTaskWithOutputMixin, DynamicWrapperTask from ..config import rnaseq_pipeline from ..platforms import IlluminaPlatform from ..rnaseq_utils import SequencingFileType, detect_layout @@ -31,6 +33,8 @@ class sra(luigi.Config): task_namespace = 'rnaseq_pipeline.sources' ncbi_public_dir: str = luigi.Parameter() + samtools_bin: str = luigi.Parameter() + bamtofastq_bin: str = luigi.Parameter() sra_config = sra() @@ -79,6 +83,12 @@ class SraRunMetadata: is_paired: bool fastq_filenames: Optional[list[str]] fastq_file_sizes: Optional[list[int]] + # Indicate if bamtofastq (from Cell Ranger) should be used to extract FASTQs from 10x BAM file(s) + use_bamtofastq: bool + # BAM file(s) to extract FASTQs from + bam_filenames: Optional[list[str]] + # Expected FASTQ filenames resulting from bamtofastq on the BAM file(s) + bam_fastq_filenames: Optional[list[str]] # currently only available if --readTypes options were passed to the fastq-load.py loader, I'd like to know if this # is stored elsewhere though, because I can see it in the UI. read_types: Optional[list[SraReadType]] @@ -123,11 +133,13 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: is_paired = root.find( 'EXPERIMENT_PACKAGE/EXPERIMENT[@accession=\'' + srx + '\']/DESIGN/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/PAIRED') is not None - sra_files = run.findall('SRAFiles/SRAFile[@semantic_name=\'fastq\']') + sra_fastq_files = run.findall('SRAFiles/SRAFile[@semantic_name=\'fastq\']') + + sra_10x_bam_files = run.findall('SRAFiles/SRAFile[@semantic_name=\'10X Genomics bam file\']') issues = SraRunIssue(0) - if not sra_files: + if not sra_fastq_files and not sra_10x_bam_files: issues |= SraRunIssue.NO_SRA_FILES # if the data was loaded with fastq-load.py, we can obtain the order of the files from the options @@ -169,7 +181,8 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: statistics = run.find('Statistics') if statistics is not None: - number_of_spots = int(statistics.attrib['nreads']) + # this may take the value 'variable' + number_of_spots = int(statistics.attrib['nreads']) if statistics.attrib['nreads'] != 'variable' else None reads = sorted(statistics.findall('Read'), key=lambda r: int(r.attrib['index'])) spot_read_lengths = [float(r.attrib['average']) for r in reads] else: @@ -184,33 +197,42 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: # sort the SRA files to match the spots using fastq-load.py options if loader == 'fastq-load.py' and fastq_load_files: - if set(fastq_load_files) == set([sf.attrib['filename'] for sf in sra_files]): + if set(fastq_load_files) == set([sf.attrib['filename'] for sf in sra_fastq_files]): logger.info('%s: Using the arguments passed to fastq-load.py to reorder the SRA files.', srr) - sra_files = sorted(sra_files, key=lambda f: fastq_load_files.index(f.attrib['filename'])) - fastq_filenames = [sf.attrib['filename'] for sf in sra_files] - fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + sra_fastq_files = sorted(sra_fastq_files, key=lambda f: fastq_load_files.index(f.attrib['filename'])) + fastq_filenames = [sf.attrib['filename'] for sf in sra_fastq_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None read_types = fastq_load_read_types # try to add a .gz suffix to the SRA files - elif set(fastq_load_files) == set([sf.attrib['filename'] + '.gz' for sf in sra_files]): + elif set(fastq_load_files) == set([sf.attrib['filename'] + '.gz' for sf in sra_fastq_files]): logger.warning( '%s: The SRA files lack .gz extensions: %s, but still correspond to fastq-load.py options: %s, will use those to reorder the SRA files.', - srx, ', '.join(sf.attrib['filename'] for sf in sra_files), ', '.join(fastq_load_files)) - sra_files = sorted(sra_files, - key=lambda f: fastq_load_files.index(f.attrib['filename'] + '.gz')) - fastq_filenames = [sf.attrib['filename'] for sf in sra_files] - fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + srx, ', '.join(sf.attrib['filename'] for sf in sra_fastq_files), ', '.join(fastq_load_files)) + sra_fastq_files = sorted(sra_fastq_files, + key=lambda f: fastq_load_files.index(f.attrib['filename'] + '.gz')) + fastq_filenames = [sf.attrib['filename'] for sf in sra_fastq_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None read_types = fastq_load_read_types - elif sra_files: + elif sra_fastq_files: logging.warning( "%s: The SRA files: %s do not match arguments passed to fastq-load.py: %s. The filenames passed to fastq-load.py will be used instead: %s.", srr, - ', '.join(sf.attrib['filename'] for sf in sra_files), + ', '.join(sf.attrib['filename'] for sf in sra_fastq_files), ' '.join(k + '=' + v if v else 'k' for k, v in options.items()), fastq_load_files) fastq_filenames = fastq_load_files fastq_file_sizes = None + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None read_types = fastq_load_read_types issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS @@ -220,8 +242,95 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, ' '.join(k + '=' + v if v else 'k' for k, v in options.items()), ', '.join(fastq_load_files)) fastq_filenames = fastq_load_files fastq_file_sizes = None + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None read_types = fastq_load_read_types + # check for 10x BAM files + elif sra_10x_bam_files: + logging.info('%s: Using 10x Genomics BAM files do determine read layout.', srr) + # we have to read the file(s), unfortunately + bam2fastq_pattern = re.compile('10x_bam_to_fastq:(.+)\(.+\)') + + if len(sra_10x_bam_files) > 1: + # TODO: support multiple BAM files, they must share the same read layout + logger.warning('%s: Multiple 10x BAM files found, will only use the first one.', srr) + bam_file = sra_10x_bam_files[0] + + logging.info('%s: Reading 10x BAM file %s from %s...', srr, bam_file.attrib['filename'], + bam_file.attrib['url']) + # FIXME: use requests + # res = requests.get(bam_file.attrib['url'], stream=True) + curl_proc = subprocess.Popen(['curl', bam_file.attrib['url']], stdout=subprocess.PIPE, + stderr=subprocess.DEVNULL) + proc = subprocess.run([sra_config.samtools_bin, 'head'], + stdin=curl_proc.stdout, stdout=subprocess.PIPE, text=True, check=True) + + # BAM may contain multiple flowcells and lanes for a given sample + flowcells = {} + bam_read_types = [] + for line in proc.stdout.splitlines(): + tag_name, tag_value = line.split("\t", maxsplit=1) + if tag_name == '@RG': + tag_value_dict = {k: v for (k, v) in [t.split(':', maxsplit=1) for t in tag_value.split('\t')]} + if 'PU' in tag_value_dict: + *flowcell_id, lane_id = tag_value_dict['PU'].split(':') + flowcell_id = '_'.join(flowcell_id) + if flowcell_id not in flowcells: + flowcells[flowcell_id] = [] + flowcells[flowcell_id].append(int(lane_id)) + elif tag_name == '@CO' and tag_value.startswith('user command line:'): + bam_read_types = [] + elif tag_name == '@CO' and (m := bam2fastq_pattern.match(tag_value)): + assert bam_read_types is not None + read_type = SequencingFileType[m.group(1)] + bam_read_types.append(read_type) + + # map lanes to layouts + flowcells = {fc: {lane_id: bam_read_types for lane_id in lanes} for fc, lanes in flowcells.items()} + + if flowcells: + logging.info('%s: Detected read types from BAM file %s: %s', srr, bam_file.attrib['filename'], + ', '.join(rt.name for rt in bam_read_types)) + # FIXME: report FASTQ filenames for all flowcells and lanes + flowcell = next(iter(flowcells.values())) + lane_id, read_types = next(iter(flowcell.items())) + fastq_filenames = [f'bamtofastq_S1_L{lane_id:03}_{rt.name}_001.fastq.gz' + for rt in read_types] + + fastq_file_sizes = None + read_types = bam_read_types + # pairedness information is misleading for BAM files + spot_read_lengths = None + is_single_end = False + is_paired = False + use_bamtofastq = True + bam_filenames = [bam_file.attrib['filename']] + bam_fastq_filenames = [f'{flowcell}/bamtofastq_S1_L{lane:03}_{rt.name}_001.fastq.gz' + for flowcell, lanes in flowcells.items() + for lane, read_types in lanes.items() + for rt in read_types] + else: + logging.warning('%s: Failed to detect read types from BAM file, ignoring that run.', srr) + issues |= SraRunIssue.INVALID_RUN + if include_invalid_runs: + result.append(SraRunMetadata(srx, srr, + is_single_end=is_single_end, + is_paired=is_paired, + fastq_filenames=None, + fastq_file_sizes=None, + read_types=None, + number_of_spots=None, + average_read_lengths=None, + fastq_load_options=None, + use_bamtofastq=False, + bam_filenames=None, + bam_fastq_filenames=None, + layout=[], + issues=issues)) + continue + # use spot statistics to determine the order of the files by matching their sizes with the sizes of the files # this is less reliable than using the fastq-load.py options, but it is still better than nothing # we can only use this strategy if all the read sizes are different and can be related to the file sizes @@ -229,21 +338,25 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: # check if the sizes are unambiguous? read_sizes = [int(read.attrib['count']) * float(read.attrib['average']) for read in reads] if len(set(read_sizes)) == len(read_sizes): - if sra_files: + if sra_fastq_files: # sort the files according to the layout # sort the layout according to the average read size reads_by_size = [e[0] for e in sorted(enumerate(reads), key=lambda e: int(e[1].attrib['count']) * float( e[1].attrib['average']))] - files_by_size = [e[0] for e in sorted(enumerate(sra_files), key=lambda e: int(e[1].attrib['size']))] + files_by_size = [e[0] for e in + sorted(enumerate(sra_fastq_files), key=lambda e: int(e[1].attrib['size']))] if len(reads_by_size) == len(files_by_size): if reads_by_size != files_by_size: logger.info('%s: Reordering SRA files to match the read sizes in the spot...', srr) - sra_files = [sra_files[reads_by_size.index(files_by_size[i])] for i, sra_file in - enumerate(sra_files)] - fastq_filenames = [sf.attrib['filename'] for sf in sra_files] - fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + sra_fastq_files = [sra_fastq_files[reads_by_size.index(files_by_size[i])] for i, sra_file in + enumerate(sra_fastq_files)] + fastq_filenames = [sf.attrib['filename'] for sf in sra_fastq_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None read_types = None else: logger.warning( @@ -251,6 +364,9 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, len(reads_by_size), len(files_by_size)) fastq_filenames = None fastq_file_sizes = None + use_bamtofastq = False + bam_filenames = None + bam_fastq_filenames = None read_types = None issues |= SraRunIssue.MISMATCHED_READ_SIZES else: @@ -260,6 +376,9 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr) fastq_filenames = None fastq_file_sizes = None + use_bamtofastq = False + bam_filenames = None + bam_fastq_filenames = None read_types = None issues |= SraRunIssue.NO_SRA_FILES else: @@ -269,17 +388,23 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: srr, read_sizes) fastq_filenames = None fastq_file_sizes = None + use_bamtofastq = False + bam_filenames = None + bam_fastq_filenames = None read_types = None issues |= SraRunIssue.AMBIGUOUS_READ_SIZES else: issues |= SraRunIssue.INVALID_RUN - logger.info( + logger.warning( '%s: No information found that can be used to order SRA files, ignoring that run.', srr) if include_invalid_runs: - fastq_filenames = [sf.attrib['filename'] for sf in sra_files] - fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_files] + fastq_filenames = [sf.attrib['filename'] for sf in sra_fastq_files] + fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] + use_bamtofastq = False + bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_fastq_filenames = None result.append(SraRunMetadata(srx, srr, is_single_end=is_single_end, is_paired=is_paired, @@ -289,12 +414,16 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: number_of_spots=None, average_read_lengths=None, fastq_load_options=None, + use_bamtofastq=use_bamtofastq, + bam_filenames=bam_filenames, + bam_fastq_filenames=None, layout=[], issues=issues)) continue try: - layout = detect_layout(srr, fastq_filenames, fastq_file_sizes, spot_read_lengths, is_single_end, is_paired) + layout = detect_layout(srr, fastq_filenames, fastq_file_sizes, spot_read_lengths, read_types, is_single_end, + is_paired) except ValueError: logger.warning('%s: Failed to detect layout, ignoring that run.', srr, exc_info=True) if include_invalid_runs: @@ -312,6 +441,9 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: number_of_spots=number_of_spots, average_read_lengths=spot_read_lengths, fastq_load_options=options if loader == 'fastq-load.py' else None, + use_bamtofastq=use_bamtofastq, + bam_filenames=bam_filenames, + bam_fastq_filenames=bam_fastq_filenames, layout=layout, issues=issues)) return result @@ -337,6 +469,23 @@ def run(self): def output(self): return luigi.LocalTarget(join(sra_config.ncbi_public_dir, 'sra', f'{self.srr}.sra')) +class DownloadSraFile(ScheduledExternalProgramTask): + """Download a SRA file.""" + srr: str = luigi.Parameter(description='SRA run identifier') + filename = luigi.Parameter(description='SRA filename') + pass + +class BamToFastq(ScheduledExternalProgramTask): + bam_file: str = luigi.Parameter() + output_dir: str = luigi.Parameter() + layout: list[str] = luigi.ListParameter() + + def program_args(self): + return [sra_config.bamtofastq_bin, '--nthreads', self.cpus, self.bam_file, self.output_dir] + + def output(self): + return [luigi.LocalTarget(join(self.output_dir, ft)) for ft in self.layout] + @requires(PrefetchSraRun) class DumpSraRun(luigi.Task): """ @@ -348,6 +497,9 @@ class DumpSraRun(luigi.Task): layout: list[str] = luigi.ListParameter(positional=False, description='Indicate the type of each output file from the run. Possible values are I1, I2, R1 and R2.') + use_bamtofastq: bool = luigi.BoolParameter(positional=False, default=False, + description='Use bamtofastq to extract FASTQs from 10x BAM files.') + metadata: dict def on_success(self): @@ -357,22 +509,30 @@ def on_success(self): return super().on_success() def run(self): - yield sratoolkit.FastqDump(input_file=self.input().path, - output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), - split='files', - number_of_reads_per_spot=len(self.layout), - metadata=self.metadata) + if self.use_bamtofastq: + download_sra_file_task = DownloadSraFile() + yield download_sra_file_task + bamtofastq_task = BamToFastq(input_file=download_sra_file_task.output().path, + output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), + layout=self.layout) + yield bamtofastq_task + # rename output files to match fastq-dump output + for i, p in enumerate(bamtofastq_task.output()): + p.move(join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), self.srr + '_' + str(i + 1) + '.fastq.gz') + else: + yield sratoolkit.FastqDump(input_file=self.input().path, + output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), + split='files', + number_of_reads_per_spot=len(self.layout), + metadata=self.metadata) if not self.complete(): raise RuntimeError( f'{repr(self)} was not completed after successful fastq-dump execution; are the output files respecting the following layout: {self.layout}?') def output(self): output_dir = join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx) - expected_files = len(self.layout) - if expected_files > 1: - return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '_' + str(i) + '.fastq.gz') for i in - range(1, expected_files + 1)], self.layout) - return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '.fastq.gz')], self.layout) + return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '_' + str(i + 1) + '.fastq.gz') for i in + range(len(self.layout))], self.layout) class EmptyRunInfoError(Exception): pass @@ -426,8 +586,6 @@ class DownloadSraExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): metadata: dict - unpack_singleton = False - @property def sample_id(self): return self.srx @@ -450,8 +608,8 @@ def run(self): if 'sample_id' not in metadata: metadata['sample_id'] = self.sample_id - for row in meta: - yield DumpSraRun(srr=row.srr, srx=self.srx, layout=[ft.name for ft in row.layout], metadata=metadata) + yield [DumpSraRun(srr=row.srr, srx=self.srx, layout=[ft.name for ft in row.layout], metadata=metadata) + for row in meta] class DownloadSraProjectRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task): """ diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 11c0ffa..86f1531 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -1,38 +1,47 @@ import datetime import logging -import os +import os.path import tempfile import uuid from glob import glob -from os.path import join, dirname +from os import unlink, makedirs, link, symlink +from os.path import dirname, join, basename import luigi import luigi.task import pandas as pd import requests +from luigi import WrapperTask +from luigi.task import flatten, flatten_output +from luigi.util import requires + from bioluigi.scheduled_external_program import ScheduledExternalProgramTask from bioluigi.tasks import fastqc, multiqc from bioluigi.tasks.cellranger import CellRangerCount -from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, TaskWithOutputMixin, DynamicWrapperTask -from luigi.task import flatten_output, WrapperTask -from luigi.util import requires - -from .config import rnaseq_pipeline -from .gemma import GemmaCliTask, gemma +from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask +from bioluigi.tasks.utils import TaskWithOutputMixin +from rnaseq_pipeline.config import rnaseq_pipeline +from .gemma import GemmaAssayType, GemmaTaskMixin, gemma +from .gemma import GemmaCliTask from .sources.arrayexpress import DownloadArrayExpressSample, DownloadArrayExpressExperiment from .sources.gemma import DownloadGemmaExperiment -from .sources.geo import DownloadGeoSample, DownloadGeoSeries, ExtractGeoSeriesBatchInfo +from .sources.geo import DownloadGeoSample, DownloadGeoSeries +from .sources.geo import ExtractGeoSeriesBatchInfo from .sources.local import DownloadLocalSample, DownloadLocalExperiment -from .sources.sra import DownloadSraProject, DownloadSraExperiment, ExtractSraProjectBatchInfo -from .targets import GemmaDatasetPlatform, GemmaDatasetHasBatch, RsemReference -from .utils import no_retry, RerunnableTaskMixin, remove_task_output +from .sources.sra import DownloadSraProject, DownloadSraExperiment +from .sources.sra import ExtractSraProjectBatchInfo +from .targets import GemmaDatasetHasBatch +from .targets import GemmaDatasetPlatform +from .targets import RsemReference +from .utils import RerunnableTaskMixin, no_retry +from .utils import remove_task_output logger = logging.getLogger(__name__) cfg = rnaseq_pipeline() gemma_cfg = gemma() -class DownloadSample(TaskWithOutputMixin, WrapperTask): +class DownloadSample(TaskWithOutputMixin, luigi.WrapperTask): """ This is a generic task for downloading an individual sample in an experiment. @@ -65,7 +74,7 @@ def requires(self): else: raise ValueError('Unknown source for sample: {}.'.format(self.source)) -class DownloadExperiment(TaskWithOutputMixin, WrapperTask): +class DownloadExperiment(TaskWithOutputMixin, luigi.WrapperTask): """ This is a generic task that detects which kind of experiment is intended to be downloaded so that downstream tasks can process regardless of the data @@ -108,47 +117,59 @@ class TrimSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): def run(self): destdir = join(cfg.OUTPUT_DIR, 'data-trimmed', self.experiment_id, self.sample_id) - os.makedirs(destdir, exist_ok=True) + makedirs(destdir, exist_ok=True) download_sample_task = self.requires() platform = download_sample_task.requires().platform - if len(self.input()) == 1: - r1, = self.input() - yield platform.get_trim_single_end_reads_task( - r1.path, - join(destdir, os.path.basename(r1.path)), - minimum_length=self.minimum_length, - report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'), - cpus=4) - elif len(self.input()) == 2: - r1, r2 = self.input() - r1, r2 = self.input() - if self.ignore_mate == 'forward': - logger.info('Forward mate is ignored for %s.', repr(self)) - yield platform.get_trim_single_end_reads_task( - r2.path, - join(destdir, os.path.basename(r2.path)), + tasks = [] + for lane in self.input(): + if 'R3' in lane.layout or 'R4' in lane.layout: + raise NotImplementedError('Trimming more than two mates is not supported.') + elif 'R1' in lane.layout and 'R2' in lane.layout: + r1, r2 = lane.files[lane.layout.index('R1')], lane.files[lane.layout.index('R2')] + if self.ignore_mate == 'forward': + logger.info('Forward mate is ignored for %s.', repr(self)) + tasks.append(platform.get_trim_single_end_reads_task( + r2, + join(destdir, basename(r2)), + minimum_length=self.minimum_length, + report_file=join(destdir, basename(r2) + '.cutadapt.json'), + cpus=4)) + elif self.ignore_mate == 'reverse': + logger.info('Reverse mate is ignored for %s.', repr(self)) + tasks.append(platform.get_trim_single_end_reads_task( + r1, + join(destdir, basename(r1)), + minimum_length=self.minimum_length, + report_file=join(destdir, basename(r1) + '.cutadapt.json'), + cpus=4)) + else: + tasks.append(platform.get_trim_paired_reads_task( + r1, r2, + join(destdir, basename(r1)), + join(destdir, basename(r2)), + minimum_length=self.minimum_length, + report_file=join(destdir, basename(r1) + '___' + basename(r2) + '.cutadapt.json'), + cpus=4)) + elif 'R1' in lane.layout: + r1 = lane.files[lane.layout.index('R1')] + tasks.append(platform.get_trim_single_end_reads_task( + r1, + join(destdir, basename(r1)), minimum_length=self.minimum_length, - report_file=join(destdir, os.path.basename(r2.path) + '.cutadapt.json'), - cpus=4) - elif self.ignore_mate == 'reverse': - logger.info('Reverse mate is ignored for %s.', repr(self)) - yield platform.get_trim_single_end_reads_task( - r1.path, - join(destdir, os.path.basename(r1.path)), + report_file=join(destdir, basename(r1) + '.cutadapt.json'), + cpus=4)) + elif 'R2' in lane.layout: + logging.warning('Found an unpaired reverse read in run %s, will treat it as single-end.', lane.run_id) + r2 = lane.files[lane.layout.index('R2')] + tasks.append(platform.get_trim_single_end_reads_task( + r2, + join(destdir, basename(r2)), minimum_length=self.minimum_length, - report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'), - cpus=4) + report_file=join(destdir, basename(r2) + '.cutadapt.json'), + cpus=4)) else: - yield platform.get_trim_paired_reads_task( - r1.path, r2.path, - join(destdir, os.path.basename(r1.path)), - join(destdir, os.path.basename(r2.path)), - minimum_length=self.minimum_length, - report_file=join(destdir, - os.path.basename(r1.path) + '_' + os.path.basename(r2.path) + '.cutadapt.json'), - cpus=4) - else: - raise NotImplementedError('Trimming more than two mates is not supported.') + raise NotImplementedError('Unsupported lane layout: ' + lane.layout + '.') + yield tasks class TrimExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ @@ -177,9 +198,9 @@ class QualityControlSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): def run(self): destdir = join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id, self.sample_id) - os.makedirs(destdir, exist_ok=True) - yield [fastqc.GenerateReport(fastq_in.path, output_dir=destdir, temp_dir=tempfile.gettempdir()) for fastq_in in - self.input()] + makedirs(destdir, exist_ok=True) + yield [fastqc.GenerateReport(fastq_in.path, output_dir=destdir, temp_dir=tempfile.gettempdir()) + for lane in self.input() for fastq_in in lane] class QualityControlExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ @@ -242,7 +263,7 @@ def program_args(self): return args def run(self): - os.makedirs(self.output().path, exist_ok=True) + makedirs(self.output().path, exist_ok=True) return super().run() def output(self): @@ -299,16 +320,13 @@ def program_args(self): forward_reads = [] reverse_reads = [] for run in runs: - if 'R1' in run.layout and 'R2' in run.layout: - forward_reads.append(run.files[run.layout.index('R1')]) - reverse_reads.append(run.files[run.layout.index('R2')]) - elif 'R1' in run.layout: - forward_reads.append(run.files[run.layout.index('R1')]) - elif 'R2' in run.layout: - logging.warning('Found an unpaired reverse read in run %s, will treat it as single-end.', run.run_id) - forward_reads.append(run.files[run.layout.index('R1')]) + if len(run) == 2: + forward_reads.append(run[0]) + reverse_reads.append(run[1]) + elif len(run) == 1: + forward_reads.append(run[0]) else: - logger.warning("Unsupported layout for run %s, it will be ignored.", run.run_id) + raise NotImplementedError("Only single or paired-end sequencing is supported.") if not forward_reads: raise ValueError('No forward reads found in the input runs. Please check the input data.') @@ -371,33 +389,18 @@ class GenerateReportForExperiment(RerunnableTaskMixin, luigi.Task): reference_id: str def run(self): - fastqc_dir = join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id) - search_dirs = [ - join(cfg.OUTPUT_DIR, 'data-trimmed', self.experiment_id), - fastqc_dir, - join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, self.reference_id, self.experiment_id)] + trim_sample_dirs, qc_sample_dirs, align_sample_dirs = self.input() + search_dirs = set() + search_dirs.update(dirname(out.path) for out in flatten(trim_sample_dirs)) + search_dirs.update(dirname(out.path) for out in flatten(qc_sample_dirs)), + search_dirs.update(dirname(out.path) for out in flatten(align_sample_dirs)) self.output().makedirs() - - # generate sample mapping for FastQC files - fastqc_suffix = '_fastqc.zip' - sample_names_file = join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id, 'sample_names.tsv') + sample_names_file = join(dirname(self.output().path), 'sample_names.tsv') with open(sample_names_file, 'w') as out: - for root, dirs, files in os.walk(fastqc_dir): - for f in files: - if f.endswith(fastqc_suffix): - fastqc_sample_id = f[:-len(fastqc_suffix)] - sample_id = os.path.basename(root) - # To avoid sample name clashes for paired-read - # sequencing, we need to add a suffix to the sample ID - # In single-end sequencing, fastq-dump does not - # produces _1, _2 suffixes, so the FastQC metrics will - # appear in the same row - if fastqc_sample_id.endswith('_1'): - sample_id += '_1' - elif fastqc_sample_id.endswith('_2'): - sample_id += '_2' - out.write(f'{fastqc_sample_id}\t{sample_id}\n') - + for lane_qc in flatten(qc_sample_dirs): + run_id = basename(lane_qc.path).removesuffix('_fastqc.html') + sample_id = basename(dirname(lane_qc.path)) + out.write(f'{run_id}\t{sample_id}_{run_id}\n') yield multiqc.GenerateReport(input_dirs=search_dirs, output_dir=dirname(self.output().path), replace_names=sample_names_file, @@ -424,7 +427,7 @@ class CountExperiment(luigi.Task): def run(self): # FIXME: find a better way to obtain the sample identifier # Each DownloadSample-like tasks have a sample_id property! Use that! - keys = [os.path.basename(f.path).replace(f'.{self.scope}.results', '') for f in self.input()] + keys = [basename(f.path).replace(f'.{self.scope}.results', '') for f in self.input()] counts_buffer = pd.concat([pd.read_csv(f.path, sep='\t', index_col=0).expected_count for f in self.input()], keys=keys, axis=1).to_csv(sep='\t') @@ -456,19 +459,20 @@ class OrganizeSingleCellSample(luigi.Task): def run(self): runs = self.input() - os.makedirs(self.output().path) + makedirs(self.output().path) for lane, run in enumerate(runs): for f, read_type in zip(run.files, run.layout): dest = join(self.output().path, f'{self.sample_id}_S1_L{lane + 1:03}_{read_type}_001.fastq.gz') if os.path.exists(dest): - os.unlink(dest) - os.link(f, dest) + unlink(dest) + link(f, dest) def output(self): return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'data-single-cell', self.experiment_id, self.sample_id)) @requires(OrganizeSingleCellSample, PrepareSingleCellReference) class AlignSingleCellSample(DynamicWrapperTask): + reference_id: str experiment_id: str sample_id: str @@ -480,8 +484,9 @@ def run(self): fastqs_dir=fastqs_dir, output_dir=self.output().path, # TODO: add an avx feature on slurm - scheduler_extra_args=['--constraint', 'thrd64'] - ) + scheduler_extra_args=['--constraint', 'thrd64'], + walltime=datetime.timedelta(days=1) + ) def output(self): return luigi.LocalTarget( @@ -509,30 +514,36 @@ class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaCliTask): Submit the batch information of an experiment to Gemma. """ - subcommand = 'fillBatchInfo' - - resources = {'submit_batch_info_jobs': 1} - - ignored_samples = luigi.ListParameter(default=[]) +@requires(AlignSingleCellExperiment, TrimExperiment, QualityControlExperiment) +class GenerateReportForSingleCellExperiment(RerunnableTaskMixin, luigi.Task): + """Generate a report for single-cell""" + experiment_id: str + reference_id: str - def requires(self): - # TODO: Have a generic strategy for extracting batch info that would - # work for all sources - if self.external_database == 'GEO': - return ExtractGeoSeriesBatchInfo(self.accession, metadata=dict(experiment_id=self.experiment_id), - ignored_samples=self.ignored_samples) - elif self.external_database == 'SRA': - return ExtractSraProjectBatchInfo(self.accession, metadata=dict(experiment_id=self.experiment_id), - ignored_samples=self.ignored_samples) - else: - raise NotImplementedError( - 'Extracting batch information from {} is not supported.'.format(self.external_database)) + def run(self): + align_sample_dirs, trim_sample_dirs, qc_sample_dirs = self.input() + search_dirs = set() + search_dirs.update(dirname(out.path) for out in flatten(align_sample_dirs)) + search_dirs.update(dirname(out.path) for out in flatten(trim_sample_dirs)) + search_dirs.update(dirname(out.path) for out in flatten(qc_sample_dirs)) + self.output().makedirs() + sample_names_file = join(dirname(self.output().path), 'sample_names.tsv') + with open(sample_names_file, 'w') as out: + for lane_qc in flatten(qc_sample_dirs): + run_id = basename(lane_qc.path).removesuffix('_fastqc.html') + sample_id = basename(dirname(lane_qc.path)) + out.write(f'{run_id}\t{sample_id}_{run_id}\n') + yield multiqc.GenerateReport(input_dirs=search_dirs, + output_dir=dirname(self.output().path), + replace_names=sample_names_file, + force=self.rerun) def output(self): - return GemmaDatasetHasBatch(self.experiment_id) + return luigi.LocalTarget( + join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id, 'multiqc_report.html')) @no_retry -class SubmitExperimentDataToGemma(RerunnableTaskMixin, GemmaCliTask): +class SubmitBulkExperimentDataToGemma(RerunnableTaskMixin, GemmaCliTask): """ Submit an experiment to Gemma. @@ -563,6 +574,78 @@ def subcommand_args(self): def output(self): return GemmaDatasetPlatform(self.experiment_id, self.platform_short_name) +class SubmitSingleCellExperimentDataToGemma(GemmaCliTask): + subcommand = 'loadSingleCellData' + + resources = {'submit_data_jobs': 1} + + def requires(self): + return AlignSingleCellExperiment(experiment_id=self.experiment_id, + reference_id=self.single_cell_reference_id, + source='gemma') + + def subcommand_args(self): + return ['-a', self.platform_short_name, + '--data-path', self._data_dir, + '--data-type', 'MEX', + '--quantitation-type-recomputed-from-raw-data', + '--preferred-quantitation-type', + # TODO: add sequencing metadata + # FIXME: add --replace + ] + + def run(self): + with tempfile.TemporaryDirectory() as self._data_dir: + for sample_dir in self.input(): + new_sample_dir = join(self._data_dir, basename(sample_dir.path)) + makedirs(new_sample_dir) + symlink(join(sample_dir.path, 'outs/filtered_feature_bc_matrix/barcodes.tsv.gz'), + join(new_sample_dir, 'barcodes.tsv.gz')) + symlink(join(sample_dir.path, 'outs/filtered_feature_bc_matrix/features.tsv.gz'), + join(new_sample_dir, 'features.tsv.gz')) + symlink(join(sample_dir.path, 'outs/filtered_feature_bc_matrix/matrix.mtx.gz'), + join(new_sample_dir, 'matrix.mtx.gz')) + super().run() + + def output(self): + return GemmaDatasetPlatform(self.experiment_id, self.platform_short_name) + +class SubmitExperimentDataToGemma(GemmaTaskMixin, WrapperTask): + def requires(self): + if self.assay_type == GemmaAssayType.BULK_RNA_SEQ: + return SubmitBulkExperimentDataToGemma(experiment_id=self.experiment_id) + elif self.assay_type == GemmaAssayType.SINGLE_CELL_RNA_SEQ: + return SubmitSingleCellExperimentDataToGemma(experiment_id=self.experiment_id) + else: + raise NotImplementedError('Loading ' + self.assay_type + ' data to Gemma is not implemented.') + +class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaCliTask): + """ + Submit the batch information of an experiment to Gemma. + """ + + subcommand = 'fillBatchInfo' + + resources = {'submit_batch_info_jobs': 1} + + ignored_samples = luigi.ListParameter(default=[]) + + def requires(self): + # TODO: Have a generic strategy for extracting batch info that would + # work for all sources + if self.external_database == 'GEO': + return ExtractGeoSeriesBatchInfo(self.accession, metadata=dict(experiment_id=self.experiment_id), + ignored_samples=self.ignored_samples) + elif self.external_database == 'SRA': + return ExtractSraProjectBatchInfo(self.accession, metadata=dict(experiment_id=self.experiment_id), + ignored_samples=self.ignored_samples) + else: + raise NotImplementedError( + 'Extracting batch information from {} is not supported.'.format(self.external_database)) + + def output(self): + return GemmaDatasetHasBatch(self.experiment_id) + class SubmitExperimentReportToGemma(RerunnableTaskMixin, GemmaCliTask): """ Submit an experiment QC report to Gemma. @@ -572,11 +655,19 @@ class SubmitExperimentReportToGemma(RerunnableTaskMixin, GemmaCliTask): subcommand = 'addMetadataFile' def requires(self): - return GenerateReportForExperiment(self.experiment_id, - taxon=self.taxon, - reference_id=self.reference_id, - source='gemma', - rerun=self.rerun) + if self.assay_type == GemmaAssayType.BULK_RNA_SEQ: + return GenerateReportForExperiment(self.experiment_id, + taxon=self.taxon, + reference_id=self.reference_id, + source='gemma', + rerun=self.rerun) + elif self.assay_type == GemmaAssayType.SINGLE_CELL_RNA_SEQ: + return GenerateReportForSingleCellExperiment(self.experiment_id, + reference_id=self.single_cell_reference_id, + source='gemma', + rerun=self.rerun) + else: + raise NotImplementedError('Cannot generate report for a ' + self.assay_type + ' experiment.') def subcommand_args(self): return ['-e', self.experiment_id, '--file-type', 'MULTIQC_REPORT', '--changelog-entry', @@ -586,40 +677,13 @@ def output(self): return luigi.LocalTarget( join(gemma_cfg.appdata_dir, 'metadata', self.experiment_id, 'MultiQCReports/multiqc_report.html')) -class SubmitSingleCellExperimentDataToGemma(RerunnableTaskMixin, GemmaCliTask): - experiment_id: str = luigi.Parameter() - subcommand = 'loadSingleCellData' - - def requires(self): - return AlignSingleCellExperiment(experiment_id=self.experiment_id, - reference_id=self.single_cell_reference_id(), - source='gemma') - - def subcommand_args(self): - return ['-e', self.experiment_id, '-a', self.platform_short_name, - '--data-path', self.input().path, - '--quantitation-type-recomputed-from-raw-data', - '--preferred-quantitation-type', - # TODO: add sequencing metadata - # FIXME: add --replace - ] - @requires(SubmitExperimentDataToGemma, SubmitExperimentBatchInfoToGemma, SubmitExperimentReportToGemma) class SubmitExperimentToGemma(TaskWithOutputMixin, WrapperTask): """ Submit an experiment data, QC reports, and batch information to Gemma. - - TODO: add QC report submission """ experiment_id: str - # Makes it so that we recheck if the task is complete after 20 minutes. - # This is because Gemma Web API is caching reply for 1200 seconds, so the - # batch factor will not appear until until the query is evicted. - # See https://github.com/PavlidisLab/rnaseq-pipeline/issues/76 for details - retry_count = 1 - retry_delay = 1200 - priority = luigi.IntParameter(default=100, positional=False, significant=False) def _targets_to_remove(self): @@ -666,9 +730,9 @@ def requires(self): df = self._retrieve_dataframe() # using None, the worker will inherit the priority from this task for all its dependencies try: - return [SubmitExperimentToGemma(row.experiment_id, - priority=100 if self.ignore_priority else row.get('priority', 100), - rerun=row.get('data') == 'resubmit') + return [SubmitExperimentToGemma(experiment_id=row.experiment_id, + priority=100 if self.ignore_priority else row.get('priority', + 100)) for _, row in df.iterrows() if row.get('priority', 1) > 0] except AttributeError as e: raise Exception(f'Failed to read experiments from {self._filename()}, is it valid?') from e diff --git a/setup.py b/setup.py index b0b9dab..18c2555 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ classifiers=['License :: Public Domain'], packages=find_packages(), include_package_data=True, - install_requires=['luigi', 'python-daemon<3.0.0', 'bioluigi>=0.2.1', 'requests', 'pandas'], + install_requires=['luigi', 'python-daemon<3.0.0', 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@feature-improved-sratools-support', 'requests', 'pandas'], extras_require={ 'gsheet': ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'], 'webviewer': ['Flask', 'gunicorn']}, diff --git a/tests/test_gemma.py b/tests/test_gemma.py index a457940..a13b3f5 100644 --- a/tests/test_gemma.py +++ b/tests/test_gemma.py @@ -7,7 +7,14 @@ def test_gemma_api(): def test_gemma_task(): task = GemmaCliTask(experiment_id='GSE110256') + assert task.dataset_short_name == 'GSE110256' + assert task.assay_type == GemmaAssayType.BULK_RNA_SEQ + assert task.platform_short_name == 'Generic_mouse_ncbiIds' env = task.program_environment() assert 'JAVA_OPTS' in env assert 'JAVA_HOME' in env assert 'PATH' in env + +def test_fac_sorted_dataset(): + task = GemmaCliTask(experiment_id='GSE232833') + assert task.assay_type == GemmaAssayType.BULK_RNA_SEQ \ No newline at end of file diff --git a/tests/test_sra.py b/tests/test_sra.py index 71a59d3..374f235 100644 --- a/tests/test_sra.py +++ b/tests/test_sra.py @@ -158,21 +158,19 @@ def test_read_xml_metadata_GSE274763(): if run.srx in ('SRX25689947', 'SRX25689948', 'SRX25689949', 'SRX25689950', 'SRX25689951', 'SRX25689952', 'SRX25689953', 'SRX25689954'): continue - if not run.layout == [R1, R2, I1, I2]: - print(run.srx) + assert run.layout == [R1, R2, I1, I2] def test_read_xml_metadata_GSE181021(): """This dataset is identified as paired-end, but only has one read file (which is a BAM).""" # TODO: also GSE267933 GSE217511, GSE178257 and GSE253640 meta = read_xml_metadata(join(test_data_dir, 'GSE181021.xml')) for run in meta: - assert run.layout == [R1] + assert run.layout == [I1, R1, R2] def test_read_xml_metadata_GSE283187(): """This dataset has a sample with 3 reads (R1, R2, R3) and an index (I1).""" meta = read_xml_metadata(join(test_data_dir, 'GSE283187.xml')) for run in meta: - print(run.srr) if run.srr == 'SRR31555331': assert run.layout == [I1, R1, I2, R2] else: @@ -182,7 +180,6 @@ def test_read_xml_metadata_GSE174332(): """In this dataset, the files passed to fastq-load.py were compressed.""" meta = read_xml_metadata(join(test_data_dir, 'GSE174332.xml')) for run in meta: - print(run.srr) if run.srr == 'SRR14511669': assert run.layout == [I1, R1, R2] else: @@ -192,7 +189,6 @@ def test_read_xml_metadata_GSE104493(): """This dataset has I1 reads with zero length""" meta = read_xml_metadata(join(test_data_dir, 'GSE104493.xml')) for run in meta: - print(run.srr) assert run.layout == [I1, R1] assert run.average_read_lengths[0] == 0.0 @@ -206,7 +202,6 @@ def test_read_xml_metadata_GSE128117(): """This dataset has a sample with 3 reads (R1, R2, R3) and an index (I1).""" meta = read_xml_metadata(join(test_data_dir, 'GSE128117.xml')) for run in meta: - print(run.srr) assert run.layout == [R1, I1] def test_read_xml_metadata_SRX26261721(): @@ -232,6 +227,55 @@ def test_read_xml_metadata_SRX26261721(): assert meta[1].layout == [SequencingFileType.I1, SequencingFileType.I2, SequencingFileType.R1, SequencingFileType.R2] +def test_SRX18986686(): + """This dataset has been submitted as BAMs, so we must use bamtofastq to extract FASTQs.""" + meta = read_xml_metadata(join(test_data_dir, 'SRX18986686.xml')) + assert len(meta) == 1 + for run in meta: + assert run.layout == [I1, R1, R2] + assert run.use_bamtofastq + assert run.fastq_filenames == [ + 'bamtofastq_S1_L001_I1_001.fastq.gz', + 'bamtofastq_S1_L001_R1_001.fastq.gz', + 'bamtofastq_S1_L001_R2_001.fastq.gz'] + assert (run.bam_fastq_filenames == [ + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R2_001.fastq.gz']) + def test_read_runinfo(): meta = read_runinfo(join(test_data_dir, 'SRX26261721.runinfo')) assert len(meta) == 2 From 819368aa4db2bbc5246f8af0119cbc9f66439479 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:14:59 -0700 Subject: [PATCH 12/45] Update Python to 3.12 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 94d8d6a..d313628 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - nodefaults dependencies: -- python=3.10 +- python=3.12 - pip - cutadapt==4.8 - multiqc==1.29 From 9310e1848604a865b0f3ca895e60ddc702a88c75 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:15:17 -0700 Subject: [PATCH 13/45] Improvements for local source --- rnaseq_pipeline/platforms.py | 7 +++++++ rnaseq_pipeline/sources/local.py | 27 +++++++++++++++++---------- 2 files changed, 24 insertions(+), 10 deletions(-) diff --git a/rnaseq_pipeline/platforms.py b/rnaseq_pipeline/platforms.py index 462cc61..f632918 100644 --- a/rnaseq_pipeline/platforms.py +++ b/rnaseq_pipeline/platforms.py @@ -1,6 +1,7 @@ from abc import abstractmethod, ABC from typing import Optional +import luigi from bioluigi.tasks import cutadapt class Platform(ABC): @@ -94,3 +95,9 @@ def get_trim_single_end_reads_task(self, r1, dest, **kwargs): def get_trim_paired_reads_task(self, r1, r2, r1_dest, r2_dest, **kwargs): raise NotImplementedError + +class TaskWithPlatformMixin(luigi.Task): + """Mixin for tasks that allow to specify sequencing platform.""" + platform_name: str = luigi.ChoiceParameter(default='ILLUMINA', choices=['ILLUMINA', 'BGI', 'NEXTERA'], + description='Sequencing platform used.', positional=False) + platform_instrument: str = luigi.Parameter(default='HiSeq 2500', description='Instrument model', positional=False) \ No newline at end of file diff --git a/rnaseq_pipeline/sources/local.py b/rnaseq_pipeline/sources/local.py index 20af2a6..d548eec 100644 --- a/rnaseq_pipeline/sources/local.py +++ b/rnaseq_pipeline/sources/local.py @@ -1,16 +1,15 @@ -import os from glob import glob -from os.path import join +from os.path import join, basename import luigi -from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask +from bioluigi.tasks.utils import TaskWithOutputMixin from ..config import rnaseq_pipeline -from ..platforms import IlluminaPlatform +from ..platforms import IlluminaPlatform, BgiPlatform, IlluminaNexteraPlatform, TaskWithPlatformMixin cfg = rnaseq_pipeline() -class DownloadLocalSample(luigi.Task): +class DownloadLocalSample(TaskWithPlatformMixin, luigi.Task): """ Local samples are organized by :experiment_id: to avoid name clashes across experiments. @@ -20,16 +19,24 @@ class DownloadLocalSample(luigi.Task): @property def platform(self): - return IlluminaPlatform('HiSeq 2500') + if self.platform_name == 'ILLUMINA': + return IlluminaPlatform(self.platform_instrument) + elif self.platform_name == 'BGI': + return BgiPlatform(self.platform_instrument) + elif self.platform_name == 'NEXTERA': + return IlluminaNexteraPlatform(self.platform_instrument) + else: + raise ValueError('Unsupported platform name {}.'.format(self.platform_name)) def output(self): # we sort to make sure that pair ends are in correct order return [luigi.LocalTarget(f) for f in sorted(glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, self.sample_id, '*.fastq.gz')))] -class DownloadLocalExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): +class DownloadLocalExperiment(luigi.WrapperTask, TaskWithPlatformMixin, TaskWithOutputMixin): experiment_id: str = luigi.Parameter() - def run(self): - for f in glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, '*')): - yield DownloadLocalSample(self.experiment_id, os.path.basename(f)) + def requires(self): + yield [DownloadLocalSample(self.experiment_id, basename(f), platform_name=self.platform_name, + platform_instrument=self.platform_instrument) + for f in glob(join(cfg.OUTPUT_DIR, cfg.DATA, 'local', self.experiment_id, '*'))] From f4d05888516d085a883002d8f50f5e62d2790a05 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:16:19 -0700 Subject: [PATCH 14/45] fixup! Add support for single-cell RNA-Seq datasets --- find-samples-with-multiple-lanes.py | 81 ----------------------------- 1 file changed, 81 deletions(-) delete mode 100644 find-samples-with-multiple-lanes.py diff --git a/find-samples-with-multiple-lanes.py b/find-samples-with-multiple-lanes.py deleted file mode 100644 index 58cf9a4..0000000 --- a/find-samples-with-multiple-lanes.py +++ /dev/null @@ -1,81 +0,0 @@ -import tarfile -import tempfile -from io import StringIO -from urllib.parse import urlparse, parse_qs - -import pandas as pd -import requests -from tqdm import tqdm - -from rnaseq_pipeline.miniml_utils import collect_geo_samples_info - -ns = {'miniml': 'http://www.ncbi.nlm.nih.gov/geo/info/MINiML'} - -def retrieve_geo_series_miniml_from_ftp(gse): - res = requests.get(f'https://ftp.ncbi.nlm.nih.gov/geo/series/{gse[:-3]}nnn/{gse}/miniml/{gse}_family.xml.tgz', - stream=True) - res.raise_for_status() - # we need to use a temporary file because Response.raw does not allow seeking - with tempfile.TemporaryFile() as tmp: - for chunk in res.iter_content(chunk_size=1024): - tmp.write(chunk) - tmp.seek(0) - with tarfile.open(fileobj=tmp, mode='r:gz') as fin: - reader = fin.extractfile(f'{gse}_family.xml') - return reader.read().decode('utf-8') - -def retrieve_geo_series_miniml_from_geo_query(gse): - res = requests.get('https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi', params=dict(acc=gse, form='xml', targ='gsm')) - res.raise_for_status() - return res.text - -def fetch_sra_metadata(gse): - try: - miniml = retrieve_geo_series_miniml_from_ftp(gse) - except Exception as e: - print( - f'Failed to retrieve MINiML metadata for {gse} from NCBI FTP server will attempt to use GEO directly.', - e) - try: - miniml = retrieve_geo_series_miniml_from_geo_query(gse) - except Exception as e: - print(f'Failed to retrieve MINiML metadata for {gse} from GEO query.', e) - return [] - try: - meta = collect_geo_samples_info(StringIO(miniml)) - except Exception as e: - print('Failed to parse MINiML from input: ' + miniml[:100], e) - return [] - results = [] - for gsm in meta: - platform, srx_url = meta[gsm] - srx = parse_qs(urlparse(srx_url).query)['term'][0] - results.append((gse, gsm, srx)) - return results - -with open('geo-sample-to-sra-experiment.tsv', 'wt') as f: - print('geo_series', 'geo_sample', 'sra_experiment', file=f, sep='\t', flush=True) - df = pd.read_table('gemma-rnaseq-datasets.tsv') - batch = [] - for gse in tqdm(df.geo_accession): - samples = fetch_sra_metadata(gse) - for sample in samples: - print(*sample, file=f, sep='\t', flush=True) - -# def fetch_runinfo(srx_ids): -# # fetch the SRX metadata -# return pd.read_csv(StringIO(retrieve_runinfo(srx_ids))) -# -# def print_results(samples): -# srx_ids = [s[2] for s in samples] -# try: -# results = fetch_runinfo(srx_ids) -# except Exception as e: -# print('Failed to retrieve runinfo for the following SRX IDs:', srx_ids, e) -# return -# for sample in samples: -# runs = results[results['Experiment'] == sample[2]]['Run'] -# r = sample + ('|'.join(runs), len(runs)) -# print(*r, sep='\t', flush=True) -# -# BATCH_SIZE = 100 From 46cd60e3292950c23e2c173ce062ae8e0476c39f Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:19:23 -0700 Subject: [PATCH 15/45] Mark test data as generated --- .gitattributes | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..dece22a --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +/tests/data/* linguist-generated=true From 77f595bf83780b9db1b0c2b297dbab7c8457f110 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:26:23 -0700 Subject: [PATCH 16/45] Add missing test data file --- tests/data/SRX18986686.xml | 231 +++++++++++++++++++++++++++++++++++++ 1 file changed, 231 insertions(+) create mode 100644 tests/data/SRX18986686.xml diff --git a/tests/data/SRX18986686.xml b/tests/data/SRX18986686.xml new file mode 100644 index 0000000..61d5b96 --- /dev/null +++ b/tests/data/SRX18986686.xml @@ -0,0 +1,231 @@ + + + + + + + SRX18986686 + GSM6925170_r1 + + GSM6925170: YY1R: young isochronic parabiont 1 right; Mus musculus; RNA-Seq + + + SRP416747 + PRJNA922313 + + + + + + + SRS16407751 + GSM6925170 + + + + GSM6925170 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul. For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1. + + + + + NextSeq 500 + + + + + + SRA1571992 + SUB12524123 + + + + Lee Rubin Lab, HSCRB, Harvard University + +
+ 7 Divinity Ave + Cambridge + MA + USA +
+ + Kristina + Holton + + + + + + SRP416747 + PRJNA922313 + GSE222510 + + + Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types + + Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors. Overall design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells. + GSE222510 + + + + + pubmed + 37118429 + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + YY1R: young isochronic parabiont 1 right + + 10090 + Mus musculus + + + + + bioproject + 922313 + + + + + + + source_name + brain + + + tissue + brain + + + strain + C57BL/6J + + + Sex + male + + + age + 3-4 months old + + + treatment + isochronic parabiosis + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + + + + + + SRR23031942 + GSM6925170_r1 + + + + GSM6925170_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS16407751 + SAMN32648504 + GSM6925170 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + \ No newline at end of file From 13961378e8cb3a6088e1afd60a4cd16ddc93efc9 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:32:33 -0700 Subject: [PATCH 17/45] Fix Makefile --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index ebc6aeb..8312152 100644 --- a/Makefile +++ b/Makefile @@ -16,7 +16,7 @@ install: install-python install-systemd-units install-RSEM install-scripts insta install-fish-completion: mkdir -p "${DESTDIR}/etc/fish/completions" - install data/luigi.fish "${DESTDIR}/etc/fish/completions/" + install -m644 data/luigi.fish "${DESTDIR}/etc/fish/completions/" install-scripts: $(MAKE) -C scripts install @@ -26,7 +26,7 @@ install-python: install-systemd-units: mkdir -p "${DESTDIR}/etc/systemd/system/" - install data/systemd/*.{service,timer,target} "${DESTDIR}/etc/systemd/system/" + install -m644 data/systemd/*.{service,timer} "${DESTDIR}/etc/systemd/system/" @echo "Remember to run 'systemctl override rnaseq-pipeline-viewer' and 'systemctl override rnaseq-pipeline-worker@' and set CONDA_BIN, CONDA_ENV, GEMMA_USERNAME and GEMMA_PASSWORD environment variables." install-RSEM: From 29a3cfbcf16c178baa07ab1104831ef1b7095e31 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 10:40:47 -0700 Subject: [PATCH 18/45] Replace luigi-wrapper with a simple CLI tool --- rnaseq_pipeline/cli.py | 78 ++++++++++++++++++++++++++ scripts/submit-experiment | 42 -------------- scripts/submit-experiments-from-gsheet | 39 ------------- setup.py | 2 +- 4 files changed, 79 insertions(+), 82 deletions(-) create mode 100644 rnaseq_pipeline/cli.py delete mode 100755 scripts/submit-experiment delete mode 100755 scripts/submit-experiments-from-gsheet diff --git a/rnaseq_pipeline/cli.py b/rnaseq_pipeline/cli.py new file mode 100644 index 0000000..c475cb7 --- /dev/null +++ b/rnaseq_pipeline/cli.py @@ -0,0 +1,78 @@ +import argparse +import sys +import os +from contextlib import contextmanager + +import luigi +import luigi.cmdline +import bioluigi.cli + +from rnaseq_pipeline.tasks import SubmitExperimentToGemma, SubmitExperimentsFromGoogleSpreadsheetToGemma, SubmitExperimentBatchInfoToGemma + +@contextmanager +def umask(umask): + print(f'Setting umask to 0x{umask:03o}') + prev_umask = os.umask(umask) + try: + yield None + finally: + print(f'Restoring umask to 0x{prev_umask:03o}') + os.umask(prev_umask) + +def parse_octal(s): + return int(s, 8) + + +def run_luigi_task(task, args): + with umask(args.umask): + results = luigi.build([task], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) + print(results.summary_text) + +def submit_experiment(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma') + parser.add_argument('--rerun', action='store_true', default=False, help='Rerun the experiment') + parser.add_argument('--priority', type=int, default=100) + parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--workers', type=int, default=30, help='Number of workers to use (defaults to 30)') + parser.add_argument('--local-scheduler', action='store_true', default=False) + args = parser.parse_args(argv) + run_luigi_task(SubmitExperimentToGemma(experiment_id=args.experiment_id, rerun=args.rerun, priority=args.priority), args) + +def submit_experiment_batch_info(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma') + parser.add_argument('--ignored-samples', nargs='+', default=[]) + parser.add_argument('--rerun', action='store_true', default=False, help='Rerun the experiment') + parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--workers', type=int, default=30, help='Number of workers to use (defaults to 30)') + parser.add_argument('--local-scheduler', action='store_true', default=False) + args = parser.parse_args(argv) + print(args.ignored_samples) + run_luigi_task(SubmitExperimentBatchInfoToGemma(experiment_id=args.experiment_id, ignored_samples=args.ignored_samples, rerun=args.rerun), args) + +def submit_experiments_from_gsheet(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--spreadsheet-id', required=True, help='Spreadsheet ID') + parser.add_argument('--sheet-name', required=True, help='Sheet name') + parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--workers', type=int, default=200, help='Number of workers to use (defaults to 200)') + parser.add_argument('--ignore-priority', action='store_true', help='Ignore the priority column in the spreadsheet') + parser.add_argument('--local-scheduler', action='store_true', default=False) + args = parser.parse_args(argv) + run_luigi_task(SubmitExperimentsFromGoogleSpreadsheetToGemma(args.spreadsheet_id, args.sheet_name, ignore_priority=args.ignore_priority), args) + +def main(): + if len(sys.argv) < 2: + print('Usage: rnaseq-pipeline-cli ') + sys.exit(1) + command = sys.argv[1] + if command == 'submit-experiment': + sys.exit(submit_experiment(sys.argv[2:])) + elif command == 'submit-experiment-batch-info': + sys.exit(submit_experiment_batch_info(sys.argv[2:])) + elif command == 'submit-experiments-from-gsheet': + sys.exit(submit_experiments_from_gsheet(sys.argv[2:])) + else: + print(f'Unknown command {command}. Possible values are: submit-experiment, submit-experiment-batch-info, submit-experiments-from-gsheet.') + sys.exit(1) diff --git a/scripts/submit-experiment b/scripts/submit-experiment deleted file mode 100755 index 20390d9..0000000 --- a/scripts/submit-experiment +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -import argparse -import sys -import os -from contextlib import contextmanager - -import luigi - -from rnaseq_pipeline.tasks import SubmitExperimentToGemma - -@contextmanager -def umask(umask): - print(f'Setting umask to 0x{umask:03o}') - prev_umask = os.umask(umask) - try: - yield None - finally: - print(f'Restoring umask to 0x{prev_umask:03o}') - os.umask(prev_umask) - -def parse_octal(s): - return int(s, 8) - -def main(argv): - parser = argparse.ArgumentParser() - parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma') - parser.add_argument('--resubmit-batch-info', action='store_true', help='Only resubmit batch information') - parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') - parser.add_argument('--workers', type=int, default=30, help='Number of workers to use (defaults to 30)') - parser.add_argument('--local-scheduler', action='store_true', default=False) - args = parser.parse_args(argv) - with umask(args.umask): - if args.resubmit_batch_info: - task = SubmitExperimentBatchInfoToGemma(experiment_id=args.experiment_id, rerun=True) - else: - task = SubmitExperimentToGemma(experiment_id=args.experiment_id) - results = luigi.build([task], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) - print(results.summary_text) - -if __name__ == '__main__': - sys.exit(main(sys.argv[1:])) diff --git a/scripts/submit-experiments-from-gsheet b/scripts/submit-experiments-from-gsheet deleted file mode 100755 index 6786660..0000000 --- a/scripts/submit-experiments-from-gsheet +++ /dev/null @@ -1,39 +0,0 @@ -#!/usr/bin/env python - -import argparse -import sys -import os -from contextlib import contextmanager - -import luigi - -from rnaseq_pipeline.tasks import SubmitExperimentsFromGoogleSpreadsheetToGemma - -@contextmanager -def umask(umask): - print(f'Setting umask to 0x{umask:03o}') - prev_umask = os.umask(umask) - try: - yield None - finally: - print(f'Restoring umask to 0x{prev_umask:03o}') - os.umask(prev_umask) - -def parse_octal(s): - return int(s, 8) - -def main(argv): - parser = argparse.ArgumentParser() - parser.add_argument('--spreadsheet-id', required=True, help='Spreadsheet ID') - parser.add_argument('--sheet-name', required=True, help='Sheet name') - parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') - parser.add_argument('--workers', type=int, default=200, help='Number of workers to use (defaults to 200)') - parser.add_argument('--ignore-priority', action='store_true', help='Ignore the priority column in the spreadsheet') - parser.add_argument('--local-scheduler', action='store_true', default=False) - args = parser.parse_args(argv) - with umask(args.umask): - results = luigi.build([SubmitExperimentsFromGoogleSpreadsheetToGemma(args.spreadsheet_id, args.sheet_name, ignore_priority=args.ignore_priority)], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) - print(results.summary_text) - -if __name__ == '__main__': - sys.exit(main(sys.argv[1:])) diff --git a/setup.py b/setup.py index 18c2555..e10a51e 100644 --- a/setup.py +++ b/setup.py @@ -16,4 +16,4 @@ extras_require={ 'gsheet': ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'], 'webviewer': ['Flask', 'gunicorn']}, - scripts=['scripts/luigi-wrapper', 'scripts/submit-experiments-from-gsheet', 'scripts/submit-experiment']) + entry_points={'console_scripts': ['rnaseq-pipeline-cli = rnaseq_pipeline.cli:main']}) From cb329044cbe644575d1496e8a8dae65372783b38 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 11:03:19 -0700 Subject: [PATCH 19/45] Skip fac-sorted dataset test since it's not public --- tests/test_gemma.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_gemma.py b/tests/test_gemma.py index a13b3f5..7960acc 100644 --- a/tests/test_gemma.py +++ b/tests/test_gemma.py @@ -1,3 +1,5 @@ +import pytest + from rnaseq_pipeline.gemma import * def test_gemma_api(): @@ -15,6 +17,7 @@ def test_gemma_task(): assert 'JAVA_HOME' in env assert 'PATH' in env +@pytest.mark.skip('This dataset is not public yet.') def test_fac_sorted_dataset(): task = GemmaCliTask(experiment_id='GSE232833') assert task.assay_type == GemmaAssayType.BULK_RNA_SEQ \ No newline at end of file From f8df3d2f4e5c24813f5b52e234ed4f3c6d2ddf61 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 11:45:21 -0700 Subject: [PATCH 20/45] sra: Cache BAM headers --- example.luigi.cfg | 2 ++ rnaseq_pipeline/sources/sra.py | 62 ++++++++++++++++++++-------------- 2 files changed, 39 insertions(+), 25 deletions(-) diff --git a/example.luigi.cfg b/example.luigi.cfg index 3316a03..dd3b07f 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -63,6 +63,8 @@ SLACK_WEBHOOK_URL= ncbi_public_dir=/cosmos/scratch/ncbi/public samtools_bin=samtools bamtofastq_bin=bamtofastq +# location where BAM headers downloaded from SRA will be cached +bam_headers_cache_dir=bam_headers [rnaseq_pipeline.gemma] cli_bin=gemma-cli diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 9bfad58..5a76123 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -35,6 +35,7 @@ class sra(luigi.Config): ncbi_public_dir: str = luigi.Parameter() samtools_bin: str = luigi.Parameter() bamtofastq_bin: str = luigi.Parameter() + bam_headers_cache_dir: str = luigi.Parameter() sra_config = sra() @@ -258,34 +259,46 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: logger.warning('%s: Multiple 10x BAM files found, will only use the first one.', srr) bam_file = sra_10x_bam_files[0] - logging.info('%s: Reading 10x BAM file %s from %s...', srr, bam_file.attrib['filename'], - bam_file.attrib['url']) - # FIXME: use requests - # res = requests.get(bam_file.attrib['url'], stream=True) - curl_proc = subprocess.Popen(['curl', bam_file.attrib['url']], stdout=subprocess.PIPE, - stderr=subprocess.DEVNULL) - proc = subprocess.run([sra_config.samtools_bin, 'head'], - stdin=curl_proc.stdout, stdout=subprocess.PIPE, text=True, check=True) + # cache the header of the BAM file + bam_header_file = join(cfg.OUTPUT_DIR, sra_config.bam_headers_cache_dir, srr + '.bam-header.txt') + if os.path.exists(bam_header_file): + logging.info('%s: Using cached 10x BAM header from %s...', srr, bam_header_file) + else: + logging.info('%s: Reading header from 10x BAM file %s from %s to %s...', srr, bam_file.attrib['filename'], + bam_file.attrib['url'], bam_header_file) + os.makedirs(os.path.dirname(bam_header_file), exist_ok=True) + with open(bam_header_file, 'w') as f: + # FIXME: use requests + # res = requests.get(bam_file.attrib['url'], stream=True) + curl_proc = subprocess.Popen(['curl', bam_file.attrib['url']], stdout=subprocess.PIPE, + stderr=subprocess.DEVNULL) + try: + proc = subprocess.run([sra_config.samtools_bin, 'head'], + stdin=curl_proc.stdout, stdout=f, text=True, check=True) + finally: + curl_proc.terminate() # BAM may contain multiple flowcells and lanes for a given sample flowcells = {} bam_read_types = [] - for line in proc.stdout.splitlines(): - tag_name, tag_value = line.split("\t", maxsplit=1) - if tag_name == '@RG': - tag_value_dict = {k: v for (k, v) in [t.split(':', maxsplit=1) for t in tag_value.split('\t')]} - if 'PU' in tag_value_dict: - *flowcell_id, lane_id = tag_value_dict['PU'].split(':') - flowcell_id = '_'.join(flowcell_id) - if flowcell_id not in flowcells: - flowcells[flowcell_id] = [] - flowcells[flowcell_id].append(int(lane_id)) - elif tag_name == '@CO' and tag_value.startswith('user command line:'): - bam_read_types = [] - elif tag_name == '@CO' and (m := bam2fastq_pattern.match(tag_value)): - assert bam_read_types is not None - read_type = SequencingFileType[m.group(1)] - bam_read_types.append(read_type) + with open(bam_header_file, 'r') as f: + for line in f: + line = line.rstrip() + tag_name, tag_value = line.split("\t", maxsplit=1) + if tag_name == '@RG': + tag_value_dict = {k: v for (k, v) in [t.split(':', maxsplit=1) for t in tag_value.split('\t')]} + if 'PU' in tag_value_dict: + *flowcell_id, lane_id = tag_value_dict['PU'].split(':') + flowcell_id = '_'.join(flowcell_id) + if flowcell_id not in flowcells: + flowcells[flowcell_id] = [] + flowcells[flowcell_id].append(int(lane_id)) + elif tag_name == '@CO' and tag_value.startswith('user command line:'): + bam_read_types = [] + elif tag_name == '@CO' and (m := bam2fastq_pattern.match(tag_value)): + assert bam_read_types is not None + read_type = SequencingFileType[m.group(1)] + bam_read_types.append(read_type) # map lanes to layouts flowcells = {fc: {lane_id: bam_read_types for lane_id in lanes} for fc, lanes in flowcells.items()} @@ -404,7 +417,6 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] - bam_fastq_filenames = None result.append(SraRunMetadata(srx, srr, is_single_end=is_single_end, is_paired=is_paired, From 0757134a0c30884a0fd831cbad6e5143ad6050f7 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 13:37:24 -0700 Subject: [PATCH 21/45] Delete organized single-cell data implement remove() to DownloadRunTarget --- rnaseq_pipeline/targets.py | 12 ++++++++++++ rnaseq_pipeline/tasks.py | 10 ++++++++++ 2 files changed, 22 insertions(+) diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index 0921f6e..ef62dfe 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -1,3 +1,4 @@ +import logging from datetime import timedelta from os.path import join, exists, getctime, getmtime from time import time @@ -6,6 +7,8 @@ from .gemma import GemmaApi +logger = logging.getLogger(__name__) + class RsemReference(luigi.Target): """ Represents the target of rsem-prepare-reference script. @@ -102,3 +105,12 @@ def __init__(self, run_id, files, layout): def exists(self): return all(t.exists() for t in self._targets) + + def remove(self): + for t in self._targets: + if t.exists(): + try: + t.remove() + logger.info('Removed %s.', repr(t)) + except: + logger.exception('Failed to remove %s.', repr(t)) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 86f1531..5715ab0 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -492,6 +492,13 @@ def output(self): return luigi.LocalTarget( join(cfg.OUTPUT_DIR, 'quantified-single-cell', self.reference_id, self.experiment_id, self.sample_id)) +@requires(DownloadExperiment) +class OrganizeSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): + def run(self): + download_sample_tasks = next(self.requires().run()) + yield [OrganizeSingleCellSample(experiment_id=experiment_id, sample_id=task.sample_id) + for task in download_sample_tasks] + class AlignSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): experiment_id: str = luigi.Parameter() source: str = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'sra', 'arrayexpress', 'local'], @@ -695,6 +702,9 @@ def _targets_to_remove(self): # any data resulting from trimming raw reads trim_task = TrimExperiment(self.experiment_id, source='gemma') outs.extend(flatten_output(trim_task)) + # reorganized data for the scRNA-Seq pipeline + organize_task = OrganizeSingleCellExperiment(self.experiment_id, source='gemma') + outs.extend(flatten_output(organize_task)) return outs def on_success(self): From f4877ef80a7a02462d3d722fbd16d0cec3900aca Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 13:37:59 -0700 Subject: [PATCH 22/45] Fix double-printing of the task summary --- rnaseq_pipeline/cli.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/rnaseq_pipeline/cli.py b/rnaseq_pipeline/cli.py index c475cb7..2110529 100644 --- a/rnaseq_pipeline/cli.py +++ b/rnaseq_pipeline/cli.py @@ -25,8 +25,7 @@ def parse_octal(s): def run_luigi_task(task, args): with umask(args.umask): - results = luigi.build([task], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) - print(results.summary_text) + luigi.build([task], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) def submit_experiment(argv): parser = argparse.ArgumentParser() From c31b5809a99f245c8cb3d89bea7c6836e8c0731a Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 9 Oct 2025 13:38:13 -0700 Subject: [PATCH 23/45] Use the new RNASEQ_PIPELINE_REPORT file type --- rnaseq_pipeline/tasks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 5715ab0..a6638c6 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -677,7 +677,7 @@ def requires(self): raise NotImplementedError('Cannot generate report for a ' + self.assay_type + ' experiment.') def subcommand_args(self): - return ['-e', self.experiment_id, '--file-type', 'MULTIQC_REPORT', '--changelog-entry', + return ['-e', self.experiment_id, '--file-type', 'RNASEQ_PIPELINE_REPORT', '--changelog-entry', 'Adding MultiQC report generated by the RNA-Seq pipeline', self.input().path] def output(self): From 1e25051e866afa9bb4d54a2a5ff72004ac370dcf Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 16 Oct 2025 13:36:42 -0700 Subject: [PATCH 24/45] Add wrapped tools --- README.md | 24 +- example.luigi.cfg | 5 + pytest.ini | 2 +- rnaseq_pipeline/__init__.py | 4 + rnaseq_pipeline/config.py | 2 + rnaseq_pipeline/gemma.py | 9 +- rnaseq_pipeline/rnaseq_utils.py | 9 +- rnaseq_pipeline/sources/geo.py | 3 +- rnaseq_pipeline/sources/sra.py | 234 +- rnaseq_pipeline/targets.py | 3 + rnaseq_pipeline/tasks.py | 64 +- rnaseq_pipeline/tenx_utils.py | 45 + rnaseq_pipeline/utils.py | 4 +- rnaseq_pipeline/wrapped_tools.py | 119 + scripts/forgive-and-reenable | 17 - setup.py | 10 +- tests/data/GSE271769.xml | 3796 ++++++++++++++++++++++++++++++ tests/data/GSE280524.xml | 888 +++++++ tests/data/SRX25247847.xml | 241 ++ tests/data/SRX26528278.xml | 225 ++ tests/data/YY1R.bam-header.txt | 232 ++ tests/test_sra.py | 20 + tests/test_tenx_utils.py | 54 + 23 files changed, 5860 insertions(+), 150 deletions(-) create mode 100644 rnaseq_pipeline/tenx_utils.py create mode 100644 rnaseq_pipeline/wrapped_tools.py delete mode 100755 scripts/forgive-and-reenable create mode 100644 tests/data/GSE271769.xml create mode 100644 tests/data/GSE280524.xml create mode 100644 tests/data/SRX25247847.xml create mode 100644 tests/data/SRX26528278.xml create mode 100644 tests/data/YY1R.bam-header.txt create mode 100644 tests/test_tenx_utils.py diff --git a/README.md b/README.md index 2a1c031..6659f66 100755 --- a/README.md +++ b/README.md @@ -71,8 +71,7 @@ your tasks at http://localhost:8082/. luigid ``` -For convenience, we provide a `luigi-wrapper` script that sets the `--module` -flag to `rnaseq_pipeline.tasks` for you. +For convenience, we provide a `rnaseq-pipeline-cli` tool to run high-level tasks: ```bash luigi-wrapper @@ -104,6 +103,7 @@ The output is organized as follow: pipeline-output/ genomes// # Genomic references references// # RSEM/STAR indexes + references-single-cell// # Cell Ranger references data// # FASTQs (organization is source-specific; note that GEO source uses SRA) data-qc/// # FastQC reports data-single-cell/// # Single-cell data (hard links to files from data/) @@ -148,6 +148,26 @@ pip install .[webviewer] gunicorn rnaseq_pipeline.viewer:app ``` +## Tools Wrappers + +A few wrappers are provided to make some tools run more efficiently. For this to work, you have to configure Bioluigi to +use the wrappers instead of the actual tools. + +Examples of behaviors: + + - copy the reference directory to a local scratch directory (Cell Ranger & RSEM) + - preload genome reference in shared memory and release unused ones (RSEM only) + +```ini +[bioluigi] +cellranger_bin=rnaseq-pipeline-cellranger +rsem_calculate_expression_bin=rnaseq-pipeline-rsem-calculate-expression + +[rnaseq_pipeline.wrapped_tools] +cellranger_bin=/absolute/path/to/cell/ranger/bin +rsem_calculate_expression_bin=/absolute/path/to/rsem +``` + ## Gemma integration The RNA-Seq pipeline is capable of communicating with Gemma using its [RESTful API](https://gemma.msl.ubc.ca/resources/restapidocs/). diff --git a/example.luigi.cfg b/example.luigi.cfg index dd3b07f..b9c8e96 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -54,9 +54,14 @@ BATCHINFODIR=batch-info # RSEM RSEM_DIR=contrib/RSEM +rsem_calculate_expression_bin=contrib/RSEM/rsem-calculate-expression SLACK_WEBHOOK_URL= +[rnaseq_pipeline.wrapped_tools.WrappedTools] +rsem_calculate_expression_bin=rsem-calculate-expression +cellranger_bin=cellranger + [rnaseq_pipeline.sources.sra] # location where tools like prefetch and fastq-dump will store downloaded SRA files # you can get this value with vdb-config -p diff --git a/pytest.ini b/pytest.ini index 18fcdbc..baad504 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,3 +1,3 @@ [pytest] log_cli=1 -log_cli_level=warning \ No newline at end of file +log_cli_level=info \ No newline at end of file diff --git a/rnaseq_pipeline/__init__.py b/rnaseq_pipeline/__init__.py index ba85506..405c029 100644 --- a/rnaseq_pipeline/__init__.py +++ b/rnaseq_pipeline/__init__.py @@ -1,3 +1,7 @@ import luigi luigi.auto_namespace(scope=__name__) + +from rnaseq_pipeline.tasks import * +from rnaseq_pipeline.sources.sra import * + diff --git a/rnaseq_pipeline/config.py b/rnaseq_pipeline/config.py index 6ac3ce6..c052c43 100644 --- a/rnaseq_pipeline/config.py +++ b/rnaseq_pipeline/config.py @@ -21,4 +21,6 @@ class rnaseq_pipeline(luigi.Config): RSEM_DIR: str = luigi.Parameter() + rsem_calculate_expression_bin: str = luigi.Parameter() + SLACK_WEBHOOK_URL: Optional[str] = luigi.OptionalParameter(default=None) diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py index 3465891..710ec5d 100644 --- a/rnaseq_pipeline/gemma.py +++ b/rnaseq_pipeline/gemma.py @@ -134,13 +134,15 @@ def assay_type(self): # single nucleus RNA sequencing http://www.ebi.ac.uk/efo/EFO_0009809 4 # fluorescence-activated cell sorting http://www.ebi.ac.uk/efo/EFO_0009108 2 # RIP-seq http://www.ebi.ac.uk/efo/EFO_0005310 1 + # RNA-seq of coding RNA from single cells http://www.ebi.ac.uk/efo/EFO_0005684 0 # These were pulled from Gemma on October 1st, 2025 assay_type_class_uri = 'http://purl.obolibrary.org/obo/OBI_0000070' microarray_uris = ['http://purl.obolibrary.org/obo/OBI_0001463', 'http://www.ebi.ac.uk/efo/EFO_0002768'] bulk_rnaseq_uris = ['http://purl.obolibrary.org/obo/OBI_0003090'] sc_rnaseq_uris = ['http://purl.obolibrary.org/obo/OBI_0002631', 'http://www.ebi.ac.uk/efo/EFO_0008913', - 'http://www.ebi.ac.uk/efo/EFO_0009809', 'http://purl.obolibrary.org/obo/OBI_0003109'] + 'http://www.ebi.ac.uk/efo/EFO_0009809', 'http://purl.obolibrary.org/obo/OBI_0003109', + 'http://www.ebi.ac.uk/efo/EFO_0005684'] fac_sorted_uri = 'http://www.ebi.ac.uk/efo/EFO_0009108' annotations = self._gemma_api.dataset_annotations(self.experiment_id) @@ -162,10 +164,7 @@ def assay_type(self): else: return GemmaAssayType.SINGLE_CELL_RNA_SEQ - # assume bulk - logger.warning('%s: No suitable experiment tag to determine the assay type, will assume bulk RNA-Seq.', - self.dataset_short_name) - return GemmaAssayType.BULK_RNA_SEQ + raise ValueError('No suitable experiment tag to determine the assay type .') class GemmaAssayType(enum.Enum): MICROARRAY = 0 diff --git a/rnaseq_pipeline/rnaseq_utils.py b/rnaseq_pipeline/rnaseq_utils.py index 2557bb6..59ca01f 100644 --- a/rnaseq_pipeline/rnaseq_utils.py +++ b/rnaseq_pipeline/rnaseq_utils.py @@ -1,5 +1,7 @@ """ -Utilities for inferring layouts of RNA-Seq data based on original filenames +Utilities for dealing with RNA-Seq data. + +This aim at being somewhat vendor-agnostic. Platform-specific logic should be organized in separate modules. """ import enum import logging @@ -46,8 +48,9 @@ def detect_layout(run_id: str, filenames: Optional[list[str]], return layout if layout := detect_fallback_fastq_name(run_id, filenames): - logger.warning('%s: Inferred file types: %s from file names with fallback name patterns: %s. This is highly inaccurate.', - run_id, '|'.join(l.name for l in layout), ', '.join(filenames)) + logger.warning( + '%s: Inferred file types: %s from file names with fallback name patterns: %s. This is highly inaccurate.', + run_id, '|'.join(l.name for l in layout), ', '.join(filenames)) return layout number_of_files = len(filenames) diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py index 394c918..34ce143 100644 --- a/rnaseq_pipeline/sources/geo.py +++ b/rnaseq_pipeline/sources/geo.py @@ -19,6 +19,7 @@ import requests from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask, TaskWithMetadataMixin from luigi.util import requires +from luigi.task import flatten from .sra import DownloadSraExperiment from ..config import rnaseq_pipeline @@ -189,7 +190,7 @@ def run(self): continue # TODO: find a cleaner way to obtain the SRA run accession - for run in sample.output(): + for run in flatten(sample.output()): for fastq in run.files: # strip the two extensions (.fastq.gz) fastq_name, _ = os.path.splitext(fastq) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 5a76123..21d7220 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -5,25 +5,26 @@ import gzip import logging import os -import re import subprocess import xml.etree.ElementTree as ET from dataclasses import dataclass from datetime import timedelta -from os.path import join +from os.path import join, basename from typing import Optional, List import luigi import pandas as pd -from luigi.util import requires - from bioluigi.scheduled_external_program import ScheduledExternalProgramTask -from bioluigi.tasks import sratoolkit +from bioluigi.tasks import sratoolkit, cellranger from bioluigi.tasks.utils import TaskWithMetadataMixin, DynamicTaskWithOutputMixin, DynamicWrapperTask +from luigi.util import requires + from ..config import rnaseq_pipeline from ..platforms import IlluminaPlatform from ..rnaseq_utils import SequencingFileType, detect_layout from ..targets import ExpirableLocalTarget, DownloadRunTarget +from ..tenx_utils import read_sequencing_layout_from_10x_bam_header, get_fastq_filenames_for_10x_sequencing_layout, \ + get_fastq_filename from ..utils import remove_task_output, RerunnableTaskMixin cfg = rnaseq_pipeline() @@ -88,6 +89,7 @@ class SraRunMetadata: use_bamtofastq: bool # BAM file(s) to extract FASTQs from bam_filenames: Optional[list[str]] + bam_file_urls: Optional[list[str]] # Expected FASTQ filenames resulting from bamtofastq on the BAM file(s) bam_fastq_filenames: Optional[list[str]] # currently only available if --readTypes options were passed to the fastq-load.py loader, I'd like to know if this @@ -205,6 +207,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] bam_fastq_filenames = None read_types = fastq_load_read_types @@ -219,6 +222,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] bam_fastq_filenames = None read_types = fastq_load_read_types @@ -233,6 +237,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = None use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] bam_fastq_filenames = None read_types = fastq_load_read_types issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS @@ -245,6 +250,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = None use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] bam_fastq_filenames = None read_types = fastq_load_read_types @@ -252,7 +258,6 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: elif sra_10x_bam_files: logging.info('%s: Using 10x Genomics BAM files do determine read layout.', srr) # we have to read the file(s), unfortunately - bam2fastq_pattern = re.compile('10x_bam_to_fastq:(.+)\(.+\)') if len(sra_10x_bam_files) > 1: # TODO: support multiple BAM files, they must share the same read layout @@ -260,48 +265,19 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: bam_file = sra_10x_bam_files[0] # cache the header of the BAM file - bam_header_file = join(cfg.OUTPUT_DIR, sra_config.bam_headers_cache_dir, srr + '.bam-header.txt') - if os.path.exists(bam_header_file): - logging.info('%s: Using cached 10x BAM header from %s...', srr, bam_header_file) - else: - logging.info('%s: Reading header from 10x BAM file %s from %s to %s...', srr, bam_file.attrib['filename'], - bam_file.attrib['url'], bam_header_file) - os.makedirs(os.path.dirname(bam_header_file), exist_ok=True) - with open(bam_header_file, 'w') as f: - # FIXME: use requests - # res = requests.get(bam_file.attrib['url'], stream=True) - curl_proc = subprocess.Popen(['curl', bam_file.attrib['url']], stdout=subprocess.PIPE, - stderr=subprocess.DEVNULL) - try: - proc = subprocess.run([sra_config.samtools_bin, 'head'], - stdin=curl_proc.stdout, stdout=f, text=True, check=True) - finally: - curl_proc.terminate() + bam_header_file = read_bam_header(srr, bam_file.attrib['filename'], bam_file.attrib['url']) # BAM may contain multiple flowcells and lanes for a given sample - flowcells = {} - bam_read_types = [] with open(bam_header_file, 'r') as f: - for line in f: - line = line.rstrip() - tag_name, tag_value = line.split("\t", maxsplit=1) - if tag_name == '@RG': - tag_value_dict = {k: v for (k, v) in [t.split(':', maxsplit=1) for t in tag_value.split('\t')]} - if 'PU' in tag_value_dict: - *flowcell_id, lane_id = tag_value_dict['PU'].split(':') - flowcell_id = '_'.join(flowcell_id) - if flowcell_id not in flowcells: - flowcells[flowcell_id] = [] - flowcells[flowcell_id].append(int(lane_id)) - elif tag_name == '@CO' and tag_value.startswith('user command line:'): - bam_read_types = [] - elif tag_name == '@CO' and (m := bam2fastq_pattern.match(tag_value)): - assert bam_read_types is not None - read_type = SequencingFileType[m.group(1)] - bam_read_types.append(read_type) - - # map lanes to layouts - flowcells = {fc: {lane_id: bam_read_types for lane_id in lanes} for fc, lanes in flowcells.items()} + flowcells = read_sequencing_layout_from_10x_bam_header(f) + bam_read_types = None + for flowcell in flowcells.values(): + for rt in flowcell.values(): + if bam_read_types is None: + bam_read_types = rt + elif bam_read_types != rt: + raise NotImplementedError( + 'Mixture of sequencing layouts in a single 10x BAM file are not supported.') if flowcells: logging.info('%s: Detected read types from BAM file %s: %s', srr, bam_file.attrib['filename'], @@ -320,10 +296,8 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: is_paired = False use_bamtofastq = True bam_filenames = [bam_file.attrib['filename']] - bam_fastq_filenames = [f'{flowcell}/bamtofastq_S1_L{lane:03}_{rt.name}_001.fastq.gz' - for flowcell, lanes in flowcells.items() - for lane, read_types in lanes.items() - for rt in read_types] + bam_file_urls = [bam_file.attrib['url']] + bam_fastq_filenames = get_fastq_filenames_for_10x_sequencing_layout(flowcells) else: logging.warning('%s: Failed to detect read types from BAM file, ignoring that run.', srr) issues |= SraRunIssue.INVALID_RUN @@ -339,6 +313,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_options=None, use_bamtofastq=False, bam_filenames=None, + bam_file_urls=None, bam_fastq_filenames=None, layout=[], issues=issues)) @@ -369,6 +344,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] bam_fastq_filenames = None read_types = None else: @@ -379,6 +355,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = None use_bamtofastq = False bam_filenames = None + bam_file_urls = None bam_fastq_filenames = None read_types = None issues |= SraRunIssue.MISMATCHED_READ_SIZES @@ -391,6 +368,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = None use_bamtofastq = False bam_filenames = None + bam_file_urls = None bam_fastq_filenames = None read_types = None issues |= SraRunIssue.NO_SRA_FILES @@ -403,6 +381,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = None use_bamtofastq = False bam_filenames = None + bam_file_urls = None bam_fastq_filenames = None read_types = None issues |= SraRunIssue.AMBIGUOUS_READ_SIZES @@ -417,6 +396,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_file_sizes = [int(sf.attrib['size']) for sf in sra_fastq_files] use_bamtofastq = False bam_filenames = [bf.attrib['filename'] for bf in sra_10x_bam_files] + bam_file_urls = [bf.attrib['url'] for bf in sra_10x_bam_files] result.append(SraRunMetadata(srx, srr, is_single_end=is_single_end, is_paired=is_paired, @@ -428,6 +408,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_options=None, use_bamtofastq=use_bamtofastq, bam_filenames=bam_filenames, + bam_file_urls=bam_file_urls, bam_fastq_filenames=None, layout=[], issues=issues)) @@ -455,11 +436,33 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: fastq_load_options=options if loader == 'fastq-load.py' else None, use_bamtofastq=use_bamtofastq, bam_filenames=bam_filenames, + bam_file_urls=bam_file_urls, bam_fastq_filenames=bam_fastq_filenames, layout=layout, issues=issues)) return result +def read_bam_header(srr, filename, url): + """Read and cache the header of a SRA BAM file.""" + bam_header_file = join(cfg.OUTPUT_DIR, sra_config.bam_headers_cache_dir, srr + '.bam-header.txt') + if os.path.exists(bam_header_file): + logging.info('%s: Using cached 10x BAM header from %s...', srr, bam_header_file) + else: + logging.info('%s: Reading header from 10x BAM file %s from %s to %s...', srr, + filename, url, bam_header_file) + os.makedirs(os.path.dirname(bam_header_file), exist_ok=True) + with open(bam_header_file, 'w') as f: + # FIXME: use requests + # res = requests.get(bam_file.attrib['url'], stream=True) + with subprocess.Popen(['curl', url], stdout=subprocess.PIPE, + stderr=subprocess.DEVNULL) as curl_proc: + try: + subprocess.run([sra_config.samtools_bin, 'head'], + stdin=curl_proc.stdout, stdout=f, text=True, check=True) + finally: + curl_proc.terminate() + return bam_header_file + class PrefetchSraRun(TaskWithMetadataMixin, luigi.Task): """ Prefetch a SRA run using prefetch from sratoolkit @@ -481,23 +484,6 @@ def run(self): def output(self): return luigi.LocalTarget(join(sra_config.ncbi_public_dir, 'sra', f'{self.srr}.sra')) -class DownloadSraFile(ScheduledExternalProgramTask): - """Download a SRA file.""" - srr: str = luigi.Parameter(description='SRA run identifier') - filename = luigi.Parameter(description='SRA filename') - pass - -class BamToFastq(ScheduledExternalProgramTask): - bam_file: str = luigi.Parameter() - output_dir: str = luigi.Parameter() - layout: list[str] = luigi.ListParameter() - - def program_args(self): - return [sra_config.bamtofastq_bin, '--nthreads', self.cpus, self.bam_file, self.output_dir] - - def output(self): - return [luigi.LocalTarget(join(self.output_dir, ft)) for ft in self.layout] - @requires(PrefetchSraRun) class DumpSraRun(luigi.Task): """ @@ -509,46 +495,102 @@ class DumpSraRun(luigi.Task): layout: list[str] = luigi.ListParameter(positional=False, description='Indicate the type of each output file from the run. Possible values are I1, I2, R1 and R2.') - use_bamtofastq: bool = luigi.BoolParameter(positional=False, default=False, - description='Use bamtofastq to extract FASTQs from 10x BAM files.') - metadata: dict + @property + def output_dir(self): + return join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx, self.srr) + def on_success(self): # cleanup SRA archive once dumped if it's still hanging around - dump_sra_run_task = self.requires() - remove_task_output(dump_sra_run_task) + prefetch_task = self.requires() + remove_task_output(prefetch_task) return super().on_success() def run(self): - if self.use_bamtofastq: - download_sra_file_task = DownloadSraFile() - yield download_sra_file_task - bamtofastq_task = BamToFastq(input_file=download_sra_file_task.output().path, - output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), - layout=self.layout) - yield bamtofastq_task - # rename output files to match fastq-dump output - for i, p in enumerate(bamtofastq_task.output()): - p.move(join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), self.srr + '_' + str(i + 1) + '.fastq.gz') - else: - yield sratoolkit.FastqDump(input_file=self.input().path, - output_dir=join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx), - split='files', - number_of_reads_per_spot=len(self.layout), - metadata=self.metadata) + yield sratoolkit.FastqDump(input_file=self.input().path, + output_dir=self.output_dir, + split='files', + number_of_reads_per_spot=len(self.layout), + metadata=self.metadata) if not self.complete(): raise RuntimeError( f'{repr(self)} was not completed after successful fastq-dump execution; are the output files respecting the following layout: {self.layout}?') def output(self): - output_dir = join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx) - return DownloadRunTarget(self.srr, [join(output_dir, self.srr + '_' + str(i + 1) + '.fastq.gz') for i in + return DownloadRunTarget(self.srr, [join(self.output_dir, self.srr + '_' + str(i + 1) + '.fastq.gz') for i in range(len(self.layout))], self.layout) class EmptyRunInfoError(Exception): pass +class DownloadSraFile(ScheduledExternalProgramTask): + """Download an SRA file.""" + srr: str = luigi.Parameter(description='SRA run identifier') + filename: str = luigi.Parameter(description='SRA filename') + file_url: str = luigi.Parameter(description='SRA file URL') + + scheduler_partition = 'Wormhole' + + _tmp_filename: str = None + + @property + def resources(self): + r = super().resources + r.update({'prefetch_jobs': 1}) + return r + + def run(self): + with self.output().temporary_path() as self._tmp_filename: + super().run() + + def program_args(self): + return ['curl', self.file_url, '-o', self._tmp_filename] + + def output(self): + return luigi.LocalTarget(join(cfg.OUTPUT_DIR, cfg.DATA, 'sra-files', self.srr, self.filename)) + +@requires(DownloadSraFile) +class DumpBamRun(TaskWithMetadataMixin, luigi.Task): + srx: str = luigi.Parameter() + layout: list[str] = luigi.ListParameter() + + # inherited + srr: str + filename: str + file_url: str + + _sequencing_layout = None + + @property + def sequencing_layout(self) -> dict[str, dict[int, list[SequencingFileType]]]: + if self._sequencing_layout is None: + with open(read_bam_header(self.srr, self.filename, self.file_url), 'r') as f: + self._sequencing_layout = read_sequencing_layout_from_10x_bam_header(f) + return self._sequencing_layout + + @property + def output_dir(self): + # TODO: include the SRR identifier in the directory structure + return join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx) + + def run(self): + yield cellranger.BamToFastq(input_file=self.input().path, + output_dir=self.output_dir, + cpus=4, + scheduler_extra_args=['--constraint', 'thrd64']) + if not self.complete(): + raise RuntimeError('Expected output files from bamtofastq were not produced:\n\t' + '\n\t'.join( + f for rt in self.output() for f in rt.files)) + + def output(self): + return [DownloadRunTarget(run_id=f'{self.srr}_{flowcell_id}_L{lane_id:03}', + files=[join(self.output_dir, get_fastq_filename(flowcell_id, lane_id, read_type)) + for read_type in lane], + layout=self.layout) + for flowcell_id, flowcell in self.sequencing_layout.items() + for lane_id, lane in flowcell.items()] + def retrieve_sra_metadata(sra_accession, format='runinfo'): """Retrieve a SRA runinfo using search and efetch utilities""" if isinstance(sra_accession, str): @@ -620,8 +662,18 @@ def run(self): if 'sample_id' not in metadata: metadata['sample_id'] = self.sample_id - yield [DumpSraRun(srr=row.srr, srx=self.srx, layout=[ft.name for ft in row.layout], metadata=metadata) - for row in meta] + runs = [] + + for row in meta: + if row.use_bamtofastq: + for bam_file, bam_url in zip(row.bam_filenames, row.bam_file_urls): + runs.append(DumpBamRun(srx=self.srx, srr=row.srr, filename=bam_file, file_url=bam_url, + layout=[ft.name for ft in row.layout], metadata=metadata)) + else: + runs.append( + DumpSraRun(srr=row.srr, srx=self.srx, layout=[ft.name for ft in row.layout], metadata=metadata)) + + yield runs class DownloadSraProjectRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task): """ diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index ef62dfe..3a4c175 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -114,3 +114,6 @@ def remove(self): logger.info('Removed %s.', repr(t)) except: logger.exception('Failed to remove %s.', repr(t)) + + def __repr__(self): + return f"DownloadRunTarget(run_id={self.run_id}, files={self.files}, layout={'|'.join(self.layout)})" diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index a6638c6..4976dcd 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -5,7 +5,7 @@ import uuid from glob import glob from os import unlink, makedirs, link, symlink -from os.path import dirname, join, basename +from os.path import dirname, join, basename, splitext import luigi import luigi.task @@ -48,11 +48,7 @@ class DownloadSample(TaskWithOutputMixin, luigi.WrapperTask): Note that the 'gemma' source does not provide individual samples. - The output of this task is a list of tuple of FASTQ files organized as follows: - - for single-end reads, [(R1)] - - for paired-end reads, [(R1, R2)] - - for paired-end reads with an index file, [(I1, R1, R2)] - - for paired-end reads with two index files, [(I1, I2, R1, R2)] + The output of this task is a list (or nested list) of DownloadRunTarget. """ experiment_id: str = luigi.Parameter() sample_id: str = luigi.Parameter() @@ -116,12 +112,11 @@ class TrimSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): minimum_length = luigi.IntParameter(default=25, positional=False) def run(self): - destdir = join(cfg.OUTPUT_DIR, 'data-trimmed', self.experiment_id, self.sample_id) - makedirs(destdir, exist_ok=True) download_sample_task = self.requires() platform = download_sample_task.requires().platform tasks = [] - for lane in self.input(): + for lane in flatten(self.input()): + destdir = join(cfg.OUTPUT_DIR, 'data-trimmed', self.experiment_id, self.sample_id, lane.run_id) if 'R3' in lane.layout or 'R4' in lane.layout: raise NotImplementedError('Trimming more than two mates is not supported.') elif 'R1' in lane.layout and 'R2' in lane.layout: @@ -197,11 +192,19 @@ class QualityControlSample(DynamicTaskWithOutputMixin, DynamicWrapperTask): sample_id: str def run(self): - destdir = join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id, self.sample_id) - makedirs(destdir, exist_ok=True) - yield [fastqc.GenerateReport(fastq_in.path, output_dir=destdir, temp_dir=tempfile.gettempdir()) + yield [fastqc.GenerateReport(fastq_in.path, + # for bamtofastq output, include the directory name to avoid lane collisions + output_dir=self._get_destdir(fastq_in), + temp_dir=tempfile.gettempdir()) for lane in self.input() for fastq_in in lane] + def _get_destdir(self, fastq_in: luigi.LocalTarget): + # TODO: make the run_id part of the output of TrimSample + run_id = basename(dirname(fastq_in.path)) + # fastqc output is a directory, so to make this atomic, we need a sub-directory for each file being QCed + filename = basename(fastq_in.path).removesuffix('.fastq.gz') + return join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id, self.sample_id, run_id, filename) + class QualityControlExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ Quality control all the samples in a given experiment. @@ -303,8 +306,9 @@ def _get_output_prefix(self): return join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, self.reference_id, self.experiment_id, self.sample_id) def program_args(self): - args = ['scripts/rsem-calculate-expression-wrapper', join(cfg.RSEM_DIR, 'rsem-calculate-expression'), '-p', - self.cpus] + args = [cfg.rsem_calculate_expression_bin] + + args.extend(['-p', self.cpus]) args.extend([ '--time', @@ -458,14 +462,16 @@ class OrganizeSingleCellSample(luigi.Task): sample_id: str def run(self): - runs = self.input() - makedirs(self.output().path) - for lane, run in enumerate(runs): - for f, read_type in zip(run.files, run.layout): - dest = join(self.output().path, f'{self.sample_id}_S1_L{lane + 1:03}_{read_type}_001.fastq.gz') - if os.path.exists(dest): - unlink(dest) - link(f, dest) + runs = flatten(self.input()) + with self.output().temporary_path() as output_dir: + os.makedirs(output_dir) + for lane, run in enumerate(runs): + print(run) + for f, read_type in zip(run.files, run.layout): + dest = join(output_dir, f'{self.sample_id}_S1_L{lane + 1:03}_{read_type}_001.fastq.gz') + if os.path.exists(dest): + unlink(dest) + link(f, dest) def output(self): return luigi.LocalTarget(join(cfg.OUTPUT_DIR, 'data-single-cell', self.experiment_id, self.sample_id)) @@ -484,7 +490,7 @@ def run(self): fastqs_dir=fastqs_dir, output_dir=self.output().path, # TODO: add an avx feature on slurm - scheduler_extra_args=['--constraint', 'thrd64'], + scheduler_extra_args=['--constraint', 'thrd64', '--gres=scratch=300G'], walltime=datetime.timedelta(days=1) ) @@ -496,7 +502,7 @@ def output(self): class OrganizeSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): def run(self): download_sample_tasks = next(self.requires().run()) - yield [OrganizeSingleCellSample(experiment_id=experiment_id, sample_id=task.sample_id) + yield [OrganizeSingleCellSample(experiment_id=self.experiment_id, sample_id=task.sample_id) for task in download_sample_tasks] class AlignSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): @@ -533,13 +539,17 @@ def run(self): search_dirs.update(dirname(out.path) for out in flatten(align_sample_dirs)) search_dirs.update(dirname(out.path) for out in flatten(trim_sample_dirs)) search_dirs.update(dirname(out.path) for out in flatten(qc_sample_dirs)) - self.output().makedirs() - sample_names_file = join(dirname(self.output().path), 'sample_names.tsv') + + # we used to write the sample_names.tsv file inside the directory, but that is not working anymore since writing + # MultiQC report now uses atomic write + sample_names_file = join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id + '.sample_names.tsv') + os.makedirs(dirname(sample_names_file), exist_ok=True) with open(sample_names_file, 'w') as out: for lane_qc in flatten(qc_sample_dirs): run_id = basename(lane_qc.path).removesuffix('_fastqc.html') sample_id = basename(dirname(lane_qc.path)) out.write(f'{run_id}\t{sample_id}_{run_id}\n') + yield multiqc.GenerateReport(input_dirs=search_dirs, output_dir=dirname(self.output().path), replace_names=sample_names_file, @@ -597,6 +607,8 @@ def subcommand_args(self): '--data-type', 'MEX', '--quantitation-type-recomputed-from-raw-data', '--preferred-quantitation-type', + # never filter 10x MEX data (this prevents detection of unfiltered data) + '--mex-no-10x-filter', # TODO: add sequencing metadata # FIXME: add --replace ] diff --git a/rnaseq_pipeline/tenx_utils.py b/rnaseq_pipeline/tenx_utils.py new file mode 100644 index 0000000..4bb6b10 --- /dev/null +++ b/rnaseq_pipeline/tenx_utils.py @@ -0,0 +1,45 @@ +""" +Utilities for handling 10x RNA sequencing data. +""" +import re + +from .rnaseq_utils import SequencingFileType + +bam2fastq_pattern = re.compile(r'10x_bam_to_fastq:(.+)\(.+\)') + +def read_sequencing_layout_from_10x_bam_header(f) -> dict[str, dict[int, list[SequencingFileType]]]: + """Read 10x BAM header and extract the sequencing layout. + + The header can be extracted with `samtools head`. + :return: A mapping of flowcell IDs to a mapping of lane IDs to a list of SequencingFileType. + """ + flowcells = {} + bam_read_types = [] + for line in f: + line = line.rstrip() + tag_name, tag_value = line.split("\t", maxsplit=1) + if tag_name == '@RG': + tag_value_dict = {k: v for (k, v) in [t.split(':', maxsplit=1) for t in tag_value.split('\t')]} + if 'PU' in tag_value_dict: + *flowcell_id, lane_id = tag_value_dict['PU'].split(':') + flowcell_id = '_'.join(flowcell_id) + if flowcell_id not in flowcells: + flowcells[flowcell_id] = [] + flowcells[flowcell_id].append(int(lane_id)) + elif tag_name == '@CO' and tag_value.startswith('user command line:'): + bam_read_types = [] + elif tag_name == '@CO' and (m := bam2fastq_pattern.match(tag_value)): + assert bam_read_types is not None + bam_read_types.append(SequencingFileType[m.group(1)]) + + # map lanes to layouts + return {fc: {lane_id: bam_read_types for lane_id in lanes} for fc, lanes in flowcells.items()} + +def get_fastq_filename(flowcell, lane, read_type: SequencingFileType): + return f'{flowcell}/bamtofastq_S1_L{lane:03}_{read_type.name}_001.fastq.gz' + +def get_fastq_filenames_for_10x_sequencing_layout(flowcells): + return [get_fastq_filename(flowcell, lane, rt) + for flowcell, lanes in flowcells.items() + for lane, read_types in lanes.items() + for rt in read_types] diff --git a/rnaseq_pipeline/utils.py b/rnaseq_pipeline/utils.py index d32e86a..469ca7b 100644 --- a/rnaseq_pipeline/utils.py +++ b/rnaseq_pipeline/utils.py @@ -49,7 +49,7 @@ def wrapper(cls): no_retry = max_retry(0) -class RerunnableTaskMixin: +class RerunnableTaskMixin(luigi.Task): """ Mixin for a task that can be rerun regardless of its completion status. """ @@ -68,7 +68,7 @@ def run(self): def complete(self): return (not self.rerun or self._has_rerun) and super().complete() -class CheckAfterCompleteMixin: +class CheckAfterCompleteMixin(luigi.Task): """Ensures that a task is completed after a successful run().""" def run(self): diff --git a/rnaseq_pipeline/wrapped_tools.py b/rnaseq_pipeline/wrapped_tools.py new file mode 100644 index 0000000..d761a5e --- /dev/null +++ b/rnaseq_pipeline/wrapped_tools.py @@ -0,0 +1,119 @@ +""" +This module provides various "wrapped" tools that improve the efficiency of the tools that the pipeline uses in various +fashions. + +The most common use case is to copy large reference files to a local scratch directory on the compute node, and +coordinate its copy/removal with a lockfile. +""" + +import fcntl +import os +import shutil +import subprocess +import sys +import tempfile +from contextlib import contextmanager +from os.path import join, dirname, basename + +import luigi +from luigi.contrib.external_program import ExternalProgramRunContext + +class WrappedToolsConfig(luigi.Config): + cellranger_bin: str = luigi.Parameter() + rsem_calculate_expression_bin: str = luigi.Parameter() + +cfg = WrappedToolsConfig() + +@contextmanager +def lockf(lockfile, exclusive=False): + if not os.path.exists(lockfile): + with open(lockfile, 'w'): + pass + with open(lockfile, 'w' if exclusive else 'r') as f: + fcntl.lockf(f.fileno(), fcntl.LOCK_EX if exclusive else fcntl.LOCK_SH, 0) + try: + yield f + finally: + fcntl.lockf(f.fileno(), fcntl.LOCK_UN, 0) + +def copy_directory_to_local_scratch(from_path): + """Copy a directory to a local scratch directory. Return the new directory (local) and a lockfile that can be used to """ + reference_name = basename(from_path) + new_dir = join(tempfile.gettempdir(), 'rnaseq-pipeline/references-single-cell', reference_name) + lockfile = new_dir + '.lock' + os.makedirs(dirname(new_dir), exist_ok=True) + if not os.path.exists(new_dir): + print('Copying ' + from_path + ' to a local directory ' + new_dir + '...') + with lockf(lockfile, exclusive=True): + with tempfile.TemporaryDirectory(prefix=basename(new_dir), dir=dirname(new_dir)) as tmp_dir: + tmp_dir = join(tmp_dir, basename(new_dir)) + shutil.copytree(from_path, tmp_dir) + os.rename(tmp_dir, new_dir) + else: + print('Reusing existing local reference directory ' + new_dir + '...') + return new_dir, lockfile + +def move_directory(from_dir, to_dir): + print(f'Moving {from_dir} to {to_dir}...') + if os.path.exists(to_dir): + print(f'Destination {to_dir} already exists, removing it first...') + shutil.rmtree(to_dir) + if os.path.exists(from_dir): + shutil.move(from_dir, to_dir) + +def subprocess_run(args, **kwargs): + proc = subprocess.Popen(args, **kwargs) + with ExternalProgramRunContext(proc): + proc.wait() + return proc.returncode + +def rsem_calculate_expression_wrapper(): + """Wrapper script for RSEM that copies the reference to a local temporary directory.""" + args = sys.argv.copy() + args[0] = cfg.rsem_calculate_expression_bin + if len(args) > 2 and os.path.isdir(args[-2]): + # copy the reference to local scratch + ref_dir = args[-2] + new_dir, lockfile = copy_directory_to_local_scratch(ref_dir) + args[-2] = new_dir + with lockf(lockfile) as f: + print('Final command: ' + ' '.join(args)) + os.set_inheritable(f.fileno(), True) + os.execv(args[0], args[1:]) + else: + print('Final command: ' + ' '.join(args)) + os.execv(args[0], args[1:]) + +def cellranger_wrapper(): + args = sys.argv.copy() + args[0] = cfg.cellranger_bin + lockfile = None + output_dir = None + with tempfile.TemporaryDirectory(prefix='cellranger-') as temp_dir: + print('Created a temporary directory for Cell Ranger execution: ' + temp_dir) + temp_output_dir = join(temp_dir, 'cellranger') + for i, arg in enumerate(args): + if arg == '--transcriptome': + new_dir, lockfile = copy_directory_to_local_scratch(args[i + 1]) + args[i + 1] = new_dir + elif arg.startswith('--transcriptome='): + new_dir, lockfile = copy_directory_to_local_scratch(arg.removeprefix('--transcriptome=')) + args[i] = '--transcriptome=' + new_dir + elif arg == '--output-dir': + output_dir = args[i + 1] + args[i + 1] = temp_output_dir + elif arg.startswith('--output-dir='): + output_dir = arg.removeprefix('--output-dir=') + args[i] = '--output-dir=' + temp_output_dir + print('Final command: ' + ' '.join(args)) + + if lockfile: + with lockf(lockfile, exclusive=False) as f: + returncode = subprocess_run(args, cwd=temp_dir) + else: + returncode = subprocess_run(args, cwd=temp_dir) + + if output_dir: + move_directory(join(temp_output_dir, 'outs'), join(output_dir, 'outs')) + + sys.exit(returncode) diff --git a/scripts/forgive-and-reenable b/scripts/forgive-and-reenable deleted file mode 100755 index 41f4585..0000000 --- a/scripts/forgive-and-reenable +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/sh - -# -# -# - -for task_id in $(bioluigi list --status DISABLED "$1" | cut -f 1); do - bioluigi reenable "$task_id" & -done - -wait - -for task_id in $(bioluigi list --status FAILED "$1" | cut -f 1); do - bioluigi forgive "$task_id" & -done - -wait diff --git a/setup.py b/setup.py index e10a51e..f34e11a 100644 --- a/setup.py +++ b/setup.py @@ -12,8 +12,14 @@ classifiers=['License :: Public Domain'], packages=find_packages(), include_package_data=True, - install_requires=['luigi', 'python-daemon<3.0.0', 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@feature-improved-sratools-support', 'requests', 'pandas'], + install_requires=['luigi', 'python-daemon<3.0.0', + 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@feature-improved-sratools-support', + 'requests', 'pandas'], extras_require={ 'gsheet': ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'], 'webviewer': ['Flask', 'gunicorn']}, - entry_points={'console_scripts': ['rnaseq-pipeline-cli = rnaseq_pipeline.cli:main']}) + entry_points={'console_scripts': [ + 'rnaseq-pipeline-cli = rnaseq_pipeline.cli:main', + 'rnaseq-pipeline-cellranger = rnaseq_pipeline.wrapped_tools:cellranger_wrapper', + 'rnaseq-pipeline-rsem-calculate-expression = rnaseq_pipeline.wrapped_tools:rsem_calculate_expression_wrapper' + ]}) diff --git a/tests/data/GSE271769.xml b/tests/data/GSE271769.xml new file mode 100644 index 0000000..ed2f1a2 --- /dev/null +++ b/tests/data/GSE271769.xml @@ -0,0 +1,3796 @@ + + + + + + + SRX25247850 + GSM8384875_r1 + + GSM8384875: No-TBI biological replicate 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933679 + GSM8384875 + + + + GSM8384875 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933679 + SAMN42381039 + GSM8384875 + + No-TBI biological replicate 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 3840 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + No injury control + + + time + No-TBI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933679 + SAMN42381039 + GSM8384875 + + + + + + + SRR29746838 + GSM8384875_r1 + + + + GSM8384875_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933679 + SAMN42381039 + GSM8384875 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247849 + GSM8384874_r1 + + GSM8384874: No-TBI biological replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933678 + GSM8384874 + + + + GSM8384874 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933678 + SAMN42381040 + GSM8384874 + + No-TBI biological replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 11017 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + No injury control + + + time + No-TBI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933678 + SAMN42381040 + GSM8384874 + + + + + + + SRR29746839 + GSM8384874_r1 + + + + GSM8384874_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933678 + SAMN42381040 + GSM8384874 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247848 + GSM8384873_r1 + + GSM8384873: No-TBI biological replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933677 + GSM8384873 + + + + GSM8384873 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933677 + SAMN42381041 + GSM8384873 + + No-TBI biological replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 2311 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + No injury control + + + time + No-TBI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933677 + SAMN42381041 + GSM8384873 + + + + + + + SRR29746840 + GSM8384873_r1 + + + + GSM8384873_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933677 + SAMN42381041 + GSM8384873 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247847 + GSM8384872_r1 + + GSM8384872: No-TBI biological replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933676 + GSM8384872 + + + + GSM8384872 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + No-TBI biological replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 6552 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + No injury control + + + time + No-TBI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + + + + + + SRR29746841 + GSM8384872_r1 + + + + GSM8384872_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247846 + GSM8384871_r1 + + GSM8384871: Post-TBI day 28 biological replicate 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933675 + GSM8384871 + + + + GSM8384871 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933675 + SAMN42381043 + GSM8384871 + + Post-TBI day 28 biological replicate 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 11434 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D28 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933675 + SAMN42381043 + GSM8384871 + + + + + + + SRR29746842 + GSM8384871_r1 + + + + GSM8384871_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933675 + SAMN42381043 + GSM8384871 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247845 + GSM8384870_r1 + + GSM8384870: Post-TBI day 28 biological replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933674 + GSM8384870 + + + + GSM8384870 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933674 + SAMN42381044 + GSM8384870 + + Post-TBI day 28 biological replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 12446 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D28 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933674 + SAMN42381044 + GSM8384870 + + + + + + + SRR29746843 + GSM8384870_r1 + + + + GSM8384870_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933674 + SAMN42381044 + GSM8384870 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247844 + GSM8384869_r1 + + GSM8384869: Post-TBI day 28 biological replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933673 + GSM8384869 + + + + GSM8384869 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933673 + SAMN42381045 + GSM8384869 + + Post-TBI day 28 biological replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 9273 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D28 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933673 + SAMN42381045 + GSM8384869 + + + + + + + SRR29746844 + GSM8384869_r1 + + + + GSM8384869_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933673 + SAMN42381045 + GSM8384869 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247843 + GSM8384868_r1 + + GSM8384868: Post-TBI day 28 biological replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933672 + GSM8384868 + + + + GSM8384868 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933672 + SAMN42381046 + GSM8384868 + + Post-TBI day 28 biological replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 7662 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D28 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933672 + SAMN42381046 + GSM8384868 + + + + + + + SRR29746845 + GSM8384868_r1 + + + + GSM8384868_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933672 + SAMN42381046 + GSM8384868 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247842 + GSM8384867_r1 + + GSM8384867: Post-TBI day 7 biological replicate 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933671 + GSM8384867 + + + + GSM8384867 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933671 + SAMN42381047 + GSM8384867 + + Post-TBI day 7 biological replicate 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 12402 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D7 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933671 + SAMN42381047 + GSM8384867 + + + + + + + SRR29746846 + GSM8384867_r1 + + + + GSM8384867_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933671 + SAMN42381047 + GSM8384867 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247841 + GSM8384866_r1 + + GSM8384866: Post-TBI day 7 biological replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933670 + GSM8384866 + + + + GSM8384866 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933670 + SAMN42381048 + GSM8384866 + + Post-TBI day 7 biological replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 11879 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D7 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933670 + SAMN42381048 + GSM8384866 + + + + + + + SRR29746847 + GSM8384866_r1 + + + + GSM8384866_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933670 + SAMN42381048 + GSM8384866 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247840 + GSM8384865_r1 + + GSM8384865: Post-TBI day 7 biological replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933669 + GSM8384865 + + + + GSM8384865 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933669 + SAMN42381049 + GSM8384865 + + Post-TBI day 7 biological replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 10734 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D7 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933669 + SAMN42381049 + GSM8384865 + + + + + + + SRR29746848 + GSM8384865_r1 + + + + GSM8384865_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933669 + SAMN42381049 + GSM8384865 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247839 + GSM8384864_r1 + + GSM8384864: Post-TBI day 7 biological replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933668 + GSM8384864 + + + + GSM8384864 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933668 + SAMN42381050 + GSM8384864 + + Post-TBI day 7 biological replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 12944 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D7 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933668 + SAMN42381050 + GSM8384864 + + + + + + + SRR29746849 + GSM8384864_r1 + + + + GSM8384864_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933668 + SAMN42381050 + GSM8384864 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247838 + GSM8384863_r1 + + GSM8384863: Post-TBI day 1 biological replicate 4, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933667 + GSM8384863 + + + + GSM8384863 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933667 + SAMN42381051 + GSM8384863 + + Post-TBI day 1 biological replicate 4, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 6610 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933667 + SAMN42381051 + GSM8384863 + + + + + + + SRR29746850 + GSM8384863_r1 + + + + GSM8384863_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933667 + SAMN42381051 + GSM8384863 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247837 + GSM8384862_r1 + + GSM8384862: Post-TBI day 1 biological replicate 3, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933666 + GSM8384862 + + + + GSM8384862 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933666 + SAMN42381052 + GSM8384862 + + Post-TBI day 1 biological replicate 3, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 5940 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933666 + SAMN42381052 + GSM8384862 + + + + + + + SRR29746851 + GSM8384862_r1 + + + + GSM8384862_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933666 + SAMN42381052 + GSM8384862 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247836 + GSM8384861_r1 + + GSM8384861: Post-TBI day 1 biological replicate 2, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933665 + GSM8384861 + + + + GSM8384861 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933665 + SAMN42381053 + GSM8384861 + + Post-TBI day 1 biological replicate 2, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 9048 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933665 + SAMN42381053 + GSM8384861 + + + + + + + SRR29746852 + GSM8384861_r1 + + + + GSM8384861_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933665 + SAMN42381053 + GSM8384861 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX25247835 + GSM8384860_r1 + + GSM8384860: Post-TBI day 1 biological replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933664 + GSM8384860 + + + + GSM8384860 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933664 + SAMN42381054 + GSM8384860 + + Post-TBI day 1 biological replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 5602 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + Closed skull cortical impact + + + time + D1 + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933664 + SAMN42381054 + GSM8384860 + + + + + + + SRR29746853 + GSM8384860_r1 + + + + GSM8384860_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933664 + SAMN42381054 + GSM8384860 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/GSE280524.xml b/tests/data/GSE280524.xml new file mode 100644 index 0000000..42f2783 --- /dev/null +++ b/tests/data/GSE280524.xml @@ -0,0 +1,888 @@ + + + + + + + SRX26528279 + GSM8599796_r1 + + GSM8599796: CA235, WT; Mus musculus; RNA-Seq + + + SRP541745 + GSE280524 + + + + + + + SRS23038326 + GSM8599796 + + + + GSM8599796 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics) Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation + + + + + NextSeq 500 + + + + + + SRA1999938 + SUB14823779 + + + + Edy Kim Lab, Pulmonary and Critical Care, Brigham and Women's Hospital, Harvard Medical School + +
+ 60 Fenwood Rd + Boston + MA + USA +
+ + Ana + Villasenor Altamirano + + + + + + SRP541745 + PRJNA1179339 + GSE280524 + + + Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation + + Neurological injury drives most deaths and morbidity among patients hospitalized for out-of-hospital cardiac arrest (OHCA). Despite its clinical importance, there are no effective pharmacological therapies targeting post-cardiac arrest (CA) neurological injury. Here we analyzed circulating immune cells from a large OHCA patient cohort, finding that lymphopenia independently associated with poor neurological outcomes. Single cell RNA-sequencing of immune cells showed that T cells with features of both innate T cells and natural killer (NK) cells were increased in patients with favorable neurological outcomes. We more specifically identified an early increase in circulating diverse NKT cells (dNKT) in a separate cohort of OHCA patients with good neurological outcomes. These cells harbored a diverse T cell receptor repertoire but were consistently specific for sulfatide antigen. In mice, we found that sulfatide-specific dNKT cells trafficked to the brain after CA and resuscitation. In the brains of mice lacking NKT cells (Cd1d-/-), we observed increased inflammatory chemokine and cytokine expression and accumulation of macrophages when compared with wild-type mice. Cd1d-/- mice also had increased neuronal injury, neurological dysfunction, and worse mortality after CA. To therapeutically enhance dNKT cell activity, we treated mice with sulfatide lipid after CA, showing that it improved neurological function. Together, these data show that sulfatide-specific dNKT cells are associated with good neurological outcomes after clinical OHCA and are neuroprotective in mice after CA. Strategies to enhance the number or function of dNKT cells may thus represent a treatment approach for CA. Overall design: Cardiac arrest (CA) was induced in WT or CD1d KO ten-week-old male mice on C57BL/6J with 80 ug potassium chloride per g body weight, after 8 minutes of arrest, epinephrine and ches compressions were applied for resucitation. Nuclei was extracted from hippocampus region 24 hr post CA. + GSE280524 + + + + + pubmed + 39630883 + + + + + + + SRS23038326 + SAMN44487052 + GSM8599796 + + CA235, WT + + 10090 + Mus musculus + + + + + bioproject + 1179339 + + + + + + + source_name + Hippocampus brain + + + tissue + Hippocampus brain + + + cell type + Whole tissue + + + treatment + Cardiac arrest induced with potassium chloride + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23038326 + SAMN44487052 + GSM8599796 + + + + + + + SRR31146606 + GSM8599796_r1 + + + + GSM8599796_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS23038326 + SAMN44487052 + GSM8599796 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX26528278 + GSM8599795_r1 + + GSM8599795: CA218, WT; Mus musculus; RNA-Seq + + + SRP541745 + GSE280524 + + + + + + + SRS23038325 + GSM8599795 + + + + GSM8599795 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics) Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation + + + + + NextSeq 500 + + + + + + SRA1999938 + SUB14823779 + + + + Edy Kim Lab, Pulmonary and Critical Care, Brigham and Women's Hospital, Harvard Medical School + +
+ 60 Fenwood Rd + Boston + MA + USA +
+ + Ana + Villasenor Altamirano + + + + + + SRP541745 + PRJNA1179339 + GSE280524 + + + Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation + + Neurological injury drives most deaths and morbidity among patients hospitalized for out-of-hospital cardiac arrest (OHCA). Despite its clinical importance, there are no effective pharmacological therapies targeting post-cardiac arrest (CA) neurological injury. Here we analyzed circulating immune cells from a large OHCA patient cohort, finding that lymphopenia independently associated with poor neurological outcomes. Single cell RNA-sequencing of immune cells showed that T cells with features of both innate T cells and natural killer (NK) cells were increased in patients with favorable neurological outcomes. We more specifically identified an early increase in circulating diverse NKT cells (dNKT) in a separate cohort of OHCA patients with good neurological outcomes. These cells harbored a diverse T cell receptor repertoire but were consistently specific for sulfatide antigen. In mice, we found that sulfatide-specific dNKT cells trafficked to the brain after CA and resuscitation. In the brains of mice lacking NKT cells (Cd1d-/-), we observed increased inflammatory chemokine and cytokine expression and accumulation of macrophages when compared with wild-type mice. Cd1d-/- mice also had increased neuronal injury, neurological dysfunction, and worse mortality after CA. To therapeutically enhance dNKT cell activity, we treated mice with sulfatide lipid after CA, showing that it improved neurological function. Together, these data show that sulfatide-specific dNKT cells are associated with good neurological outcomes after clinical OHCA and are neuroprotective in mice after CA. Strategies to enhance the number or function of dNKT cells may thus represent a treatment approach for CA. Overall design: Cardiac arrest (CA) was induced in WT or CD1d KO ten-week-old male mice on C57BL/6J with 80 ug potassium chloride per g body weight, after 8 minutes of arrest, epinephrine and ches compressions were applied for resucitation. Nuclei was extracted from hippocampus region 24 hr post CA. + GSE280524 + + + + + pubmed + 39630883 + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + CA218, WT + + 10090 + Mus musculus + + + + + bioproject + 1179339 + + + + + + + source_name + Hippocampus brain + + + tissue + Hippocampus brain + + + cell type + Whole tissue + + + treatment + Cardiac arrest induced with potassium chloride + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + + + + + + SRR31146607 + GSM8599795_r1 + + + + GSM8599795_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX26528277 + GSM8599794_r1 + + GSM8599794: CA207, CD1d KO; Mus musculus; RNA-Seq + + + SRP541745 + GSE280524 + + + + + + + SRS23038324 + GSM8599794 + + + + GSM8599794 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics) Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation + + + + + NextSeq 500 + + + + + + SRA1999938 + SUB14823779 + + + + Edy Kim Lab, Pulmonary and Critical Care, Brigham and Women's Hospital, Harvard Medical School + +
+ 60 Fenwood Rd + Boston + MA + USA +
+ + Ana + Villasenor Altamirano + + + + + + SRP541745 + PRJNA1179339 + GSE280524 + + + Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation + + Neurological injury drives most deaths and morbidity among patients hospitalized for out-of-hospital cardiac arrest (OHCA). Despite its clinical importance, there are no effective pharmacological therapies targeting post-cardiac arrest (CA) neurological injury. Here we analyzed circulating immune cells from a large OHCA patient cohort, finding that lymphopenia independently associated with poor neurological outcomes. Single cell RNA-sequencing of immune cells showed that T cells with features of both innate T cells and natural killer (NK) cells were increased in patients with favorable neurological outcomes. We more specifically identified an early increase in circulating diverse NKT cells (dNKT) in a separate cohort of OHCA patients with good neurological outcomes. These cells harbored a diverse T cell receptor repertoire but were consistently specific for sulfatide antigen. In mice, we found that sulfatide-specific dNKT cells trafficked to the brain after CA and resuscitation. In the brains of mice lacking NKT cells (Cd1d-/-), we observed increased inflammatory chemokine and cytokine expression and accumulation of macrophages when compared with wild-type mice. Cd1d-/- mice also had increased neuronal injury, neurological dysfunction, and worse mortality after CA. To therapeutically enhance dNKT cell activity, we treated mice with sulfatide lipid after CA, showing that it improved neurological function. Together, these data show that sulfatide-specific dNKT cells are associated with good neurological outcomes after clinical OHCA and are neuroprotective in mice after CA. Strategies to enhance the number or function of dNKT cells may thus represent a treatment approach for CA. Overall design: Cardiac arrest (CA) was induced in WT or CD1d KO ten-week-old male mice on C57BL/6J with 80 ug potassium chloride per g body weight, after 8 minutes of arrest, epinephrine and ches compressions were applied for resucitation. Nuclei was extracted from hippocampus region 24 hr post CA. + GSE280524 + + + + + pubmed + 39630883 + + + + + + + SRS23038324 + SAMN44487054 + GSM8599794 + + CA207, CD1d KO + + 10090 + Mus musculus + + + + + bioproject + 1179339 + + + + + + + source_name + Hippocampus brain + + + tissue + Hippocampus brain + + + cell type + Whole tissue + + + treatment + Cardiac arrest induced with potassium chloride + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23038324 + SAMN44487054 + GSM8599794 + + + + + + + SRR31146608 + GSM8599794_r1 + + + + GSM8599794_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS23038324 + SAMN44487054 + GSM8599794 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + + + + SRX26528276 + GSM8599793_r1 + + GSM8599793: CA223, CD1d KO; Mus musculus; RNA-Seq + + + SRP541745 + GSE280524 + + + + + + + SRS23038323 + GSM8599793 + + + + GSM8599793 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics) Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation + + + + + NextSeq 500 + + + + + + SRA1999938 + SUB14823779 + + + + Edy Kim Lab, Pulmonary and Critical Care, Brigham and Women's Hospital, Harvard Medical School + +
+ 60 Fenwood Rd + Boston + MA + USA +
+ + Ana + Villasenor Altamirano + + + + + + SRP541745 + PRJNA1179339 + GSE280524 + + + Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation + + Neurological injury drives most deaths and morbidity among patients hospitalized for out-of-hospital cardiac arrest (OHCA). Despite its clinical importance, there are no effective pharmacological therapies targeting post-cardiac arrest (CA) neurological injury. Here we analyzed circulating immune cells from a large OHCA patient cohort, finding that lymphopenia independently associated with poor neurological outcomes. Single cell RNA-sequencing of immune cells showed that T cells with features of both innate T cells and natural killer (NK) cells were increased in patients with favorable neurological outcomes. We more specifically identified an early increase in circulating diverse NKT cells (dNKT) in a separate cohort of OHCA patients with good neurological outcomes. These cells harbored a diverse T cell receptor repertoire but were consistently specific for sulfatide antigen. In mice, we found that sulfatide-specific dNKT cells trafficked to the brain after CA and resuscitation. In the brains of mice lacking NKT cells (Cd1d-/-), we observed increased inflammatory chemokine and cytokine expression and accumulation of macrophages when compared with wild-type mice. Cd1d-/- mice also had increased neuronal injury, neurological dysfunction, and worse mortality after CA. To therapeutically enhance dNKT cell activity, we treated mice with sulfatide lipid after CA, showing that it improved neurological function. Together, these data show that sulfatide-specific dNKT cells are associated with good neurological outcomes after clinical OHCA and are neuroprotective in mice after CA. Strategies to enhance the number or function of dNKT cells may thus represent a treatment approach for CA. Overall design: Cardiac arrest (CA) was induced in WT or CD1d KO ten-week-old male mice on C57BL/6J with 80 ug potassium chloride per g body weight, after 8 minutes of arrest, epinephrine and ches compressions were applied for resucitation. Nuclei was extracted from hippocampus region 24 hr post CA. + GSE280524 + + + + + pubmed + 39630883 + + + + + + + SRS23038323 + SAMN44487055 + GSM8599793 + + CA223, CD1d KO + + 10090 + Mus musculus + + + + + bioproject + 1179339 + + + + + + + source_name + Hippocampus brain + + + tissue + Hippocampus brain + + + cell type + Whole tissue + + + treatment + Cardiac arrest induced with potassium chloride + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23038323 + SAMN44487055 + GSM8599793 + + + + + + + SRR31146609 + GSM8599793_r1 + + + + GSM8599793_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS23038323 + SAMN44487055 + GSM8599793 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/SRX25247847.xml b/tests/data/SRX25247847.xml new file mode 100644 index 0000000..c6807f8 --- /dev/null +++ b/tests/data/SRX25247847.xml @@ -0,0 +1,241 @@ + + + + + + + SRX25247847 + GSM8384872_r1 + + GSM8384872: No-TBI biological replicate 1, scRNAseq; Mus musculus; RNA-Seq + + + SRP518641 + PRJNA1133059 + + + + + + + SRS21933676 + GSM8384872 + + + + GSM8384872 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Collected tissue specimens were finely chopped and digested in 5ml buffer (1mg/ml collagenase D, 100µg/ml Dnase, 5mM CaCl2, 10µl/ml papain, 10% FBS in RPMI) in a dish for 30min inside a shaker maintained at 80 RPM, 37°C. To remove any undigested fraction or tissue particles, samples were then passed through a 40uM cell strainer (pluriSelect, cat# 43-50040-01). Myelin debris were then removed using specific magnetic beads (Miltenyi Biotech, cat# 130-096-733) per manufacturer's recommended protocol. Single-cell suspensions were then fixed in buffer containing 4% paraformaldehyde per manufacturer's recommendation. Library was prepared per manufacturer's recommendation (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed cells from all samples in a given endpoint were hybridized overnight with unique probe barcode and multiplexed accordingly. Post-hybridized pool of barcoded samples were then subjected to gel bead in emulsion (GEM). Briefly, hybridized samples were resuspended in mastermix and loaded together with partitioning oil and the gel beads into the chip to generate the GEM in 10x Genomics Chromium X. Samples were recovered post-GEM generation step, subjected to brief pre-amplification PCR. The samples were retrotranscripted to cDNA, which contains an Illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. During the library construction, Dual Index Plate TS Set A from the supplied 10x Genomics reagent kit was used that contains paired-end constructs with unique P5 and P7 sequences. Samples were subjected to brief sample index PCR per manufacturer's protocol.Post sample index PCR, the specific library product size selection was made using SPRIselect. The library was subjequently analyzed and quantified in Agilant Tapestation and by KAPA library quantification kit in qPCR-based method. + + + + + NextSeq 550 + + + + + + SRA1922177 + SUB14598107 + + + + University of Wisconsin-Madison + +
+ 2500 Overlook Terrace + Madison + WI + USA +
+ + Cara + Green + + + + + + SRP518641 + PRJNA1133059 + GSE271769 + + + Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype + + TBI causes the disruption of blood vessels in brain leading to hemorrhage, edema, and changes in cerebral blood flow. How such altered vascular and flow condition affect endothelial cells, the cellular unit of blood vessels, is not known. We used single cell RNA sequencing (scRNAseq) to analyze the heterogenity in endothelial cell clusters in brain, and how key cellular and signaling signatures of these clusters are temporally changed post-TBI at the site of injury. Overall design: We used closed skull cortical impact (CCI) mouse model. The brain cortex specimens were isolated from the site of injury at day 1, 7 and 28 post-TBI. Site-matched specimens were also harvested from uninjured control mice. Single cells were harvested from the collected tissue specimens. Myelin debris was removed from the cells and the specimens were immediately fixed in 4% paraformaldehyde. Fixed samples were subjected to scRNAseq as per manufacturer's protocol. + GSE271769 + + + + + pubmed + 39605741 + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + No-TBI biological replicate 1, scRNAseq + + 10090 + Mus musculus + + + + + bioproject + 1133059 + + + + + + + source_name + Brain + + + age + 14 week + + + Sex + male + + + tissue + Brain + + + num cells_called + 6552 + + + genotype + C57BL/J (Jax ID 000668) + + + treatment + No injury control + + + time + No-TBI + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + + + + + + SRR29746841 + GSM8384872_r1 + + + + GSM8384872_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS21933676 + SAMN42381042 + GSM8384872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/SRX26528278.xml b/tests/data/SRX26528278.xml new file mode 100644 index 0000000..8ba5714 --- /dev/null +++ b/tests/data/SRX26528278.xml @@ -0,0 +1,225 @@ + + + + + + + SRX26528278 + GSM8599795_r1 + + GSM8599795: CA218, WT; Mus musculus; RNA-Seq + + + SRP541745 + GSE280524 + + + + + + + SRS23038325 + GSM8599795 + + + + GSM8599795 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + By using a biopsy punch, fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics) Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation + + + + + NextSeq 500 + + + + + + SRA1999938 + SUB14823779 + + + + Edy Kim Lab, Pulmonary and Critical Care, Brigham and Women's Hospital, Harvard Medical School + +
+ 60 Fenwood Rd + Boston + MA + USA +
+ + Ana + Villasenor Altamirano + + + + + + SRP541745 + PRJNA1179339 + GSE280524 + + + Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation + + Neurological injury drives most deaths and morbidity among patients hospitalized for out-of-hospital cardiac arrest (OHCA). Despite its clinical importance, there are no effective pharmacological therapies targeting post-cardiac arrest (CA) neurological injury. Here we analyzed circulating immune cells from a large OHCA patient cohort, finding that lymphopenia independently associated with poor neurological outcomes. Single cell RNA-sequencing of immune cells showed that T cells with features of both innate T cells and natural killer (NK) cells were increased in patients with favorable neurological outcomes. We more specifically identified an early increase in circulating diverse NKT cells (dNKT) in a separate cohort of OHCA patients with good neurological outcomes. These cells harbored a diverse T cell receptor repertoire but were consistently specific for sulfatide antigen. In mice, we found that sulfatide-specific dNKT cells trafficked to the brain after CA and resuscitation. In the brains of mice lacking NKT cells (Cd1d-/-), we observed increased inflammatory chemokine and cytokine expression and accumulation of macrophages when compared with wild-type mice. Cd1d-/- mice also had increased neuronal injury, neurological dysfunction, and worse mortality after CA. To therapeutically enhance dNKT cell activity, we treated mice with sulfatide lipid after CA, showing that it improved neurological function. Together, these data show that sulfatide-specific dNKT cells are associated with good neurological outcomes after clinical OHCA and are neuroprotective in mice after CA. Strategies to enhance the number or function of dNKT cells may thus represent a treatment approach for CA. Overall design: Cardiac arrest (CA) was induced in WT or CD1d KO ten-week-old male mice on C57BL/6J with 80 ug potassium chloride per g body weight, after 8 minutes of arrest, epinephrine and ches compressions were applied for resucitation. Nuclei was extracted from hippocampus region 24 hr post CA. + GSE280524 + + + + + pubmed + 39630883 + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + CA218, WT + + 10090 + Mus musculus + + + + + bioproject + 1179339 + + + + + + + source_name + Hippocampus brain + + + tissue + Hippocampus brain + + + cell type + Whole tissue + + + treatment + Cardiac arrest induced with potassium chloride + + + geo_loc_name + missing + + + collection_date + missing + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + + + + + + SRR31146607 + GSM8599795_r1 + + + + GSM8599795_r1 + + + + + assembly + mm10 + + + intentional_duplicate + + + + + + + SRS23038325 + SAMN44487053 + GSM8599795 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/YY1R.bam-header.txt b/tests/data/YY1R.bam-header.txt new file mode 100644 index 0000000..d76a537 --- /dev/null +++ b/tests/data/YY1R.bam-header.txt @@ -0,0 +1,232 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:195471971 +@SQ SN:10 LN:130694993 +@SQ SN:11 LN:122082543 +@SQ SN:12 LN:120129022 +@SQ SN:13 LN:120421639 +@SQ SN:14 LN:124902244 +@SQ SN:15 LN:104043685 +@SQ SN:16 LN:98207768 +@SQ SN:17 LN:94987271 +@SQ SN:18 LN:90702639 +@SQ SN:19 LN:61431566 +@SQ SN:2 LN:182113224 +@SQ SN:3 LN:160039680 +@SQ SN:4 LN:156508116 +@SQ SN:5 LN:151834684 +@SQ SN:6 LN:149736546 +@SQ SN:7 LN:145441459 +@SQ SN:8 LN:129401213 +@SQ SN:9 LN:124595110 +@SQ SN:MT LN:16299 +@SQ SN:X LN:171031299 +@SQ SN:Y LN:91744698 +@SQ SN:JH584299.1 LN:953012 +@SQ SN:GL456233.1 LN:336933 +@SQ SN:JH584301.1 LN:259875 +@SQ SN:GL456211.1 LN:241735 +@SQ SN:GL456350.1 LN:227966 +@SQ SN:JH584293.1 LN:207968 +@SQ SN:GL456221.1 LN:206961 +@SQ SN:JH584297.1 LN:205776 +@SQ SN:JH584296.1 LN:199368 +@SQ SN:GL456354.1 LN:195993 +@SQ SN:JH584294.1 LN:191905 +@SQ SN:JH584298.1 LN:184189 +@SQ SN:JH584300.1 LN:182347 +@SQ SN:GL456219.1 LN:175968 +@SQ SN:GL456210.1 LN:169725 +@SQ SN:JH584303.1 LN:158099 +@SQ SN:JH584302.1 LN:155838 +@SQ SN:GL456212.1 LN:153618 +@SQ SN:JH584304.1 LN:114452 +@SQ SN:GL456379.1 LN:72385 +@SQ SN:GL456216.1 LN:66673 +@SQ SN:GL456393.1 LN:55711 +@SQ SN:GL456366.1 LN:47073 +@SQ SN:GL456367.1 LN:42057 +@SQ SN:GL456239.1 LN:40056 +@SQ SN:GL456213.1 LN:39340 +@SQ SN:GL456383.1 LN:38659 +@SQ SN:GL456385.1 LN:35240 +@SQ SN:GL456360.1 LN:31704 +@SQ SN:GL456378.1 LN:31602 +@SQ SN:GL456389.1 LN:28772 +@SQ SN:GL456372.1 LN:28664 +@SQ SN:GL456370.1 LN:26764 +@SQ SN:GL456381.1 LN:25871 +@SQ SN:GL456387.1 LN:24685 +@SQ SN:GL456390.1 LN:24668 +@SQ SN:GL456394.1 LN:24323 +@SQ SN:GL456392.1 LN:23629 +@SQ SN:GL456382.1 LN:23158 +@SQ SN:GL456359.1 LN:22974 +@SQ SN:GL456396.1 LN:21240 +@SQ SN:GL456368.1 LN:20208 +@SQ SN:JH584292.1 LN:14945 +@SQ SN:JH584295.1 LN:1976 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--outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn 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ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn 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ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir 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--outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 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ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir 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--outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) +@CO user command line: STAR --genomeDir /seq/regev_genome_portal/SOFTWARE/10X/refdata-cellranger-1.2.0/refdata-cellranger-mm10-1.2.0/star --readFilesIn /psych/genetics_data/jlevin/nextseq_170601/combo3/10/s10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk0/files/reads.fastq/1.fastq --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:s10:MissingLibrary:1:HG3T5BGX2:1 SM:s10 LB:MissingLibrary.1 PU:s10:MissingLibrary:1:HG3T5BGX2:1 PL:ILLUMINA +@CO 10x_bam_to_fastq:I1(BC:QT) +@CO 10x_bam_to_fastq:R1(CR:CY,UR:UY,TR:TQ) +@CO 10x_bam_to_fastq:R2(SEQ:QUAL) diff --git a/tests/test_sra.py b/tests/test_sra.py index 374f235..956477e 100644 --- a/tests/test_sra.py +++ b/tests/test_sra.py @@ -276,6 +276,26 @@ def test_SRX18986686(): 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R1_001.fastq.gz', 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R2_001.fastq.gz']) +@pytest.mark.skip('This run lacks statistics, reach out to SRA curators?') +def test_SRX17676975(): + runs = read_xml_metadata(join(test_data_dir, 'SRX17676975.xml')) + assert len(runs) == 9 + +def test_GSE271769(): + runs = read_xml_metadata(join(test_data_dir, 'GSE271769.xml')) + assert len(runs) == 9 + + task = DownloadSraExperiment(srx='SRX25247848') + task.run() + +def test_SRX25247847(): + runs = read_xml_metadata(join(test_data_dir, 'SRX25247847.xml')) + assert len(runs) == 1 + +def test_SRX26528278(): + runs = read_xml_metadata(join(test_data_dir, 'SRX26528278.xml')) + assert len(runs) == 1 + def test_read_runinfo(): meta = read_runinfo(join(test_data_dir, 'SRX26261721.runinfo')) assert len(meta) == 2 diff --git a/tests/test_tenx_utils.py b/tests/test_tenx_utils.py new file mode 100644 index 0000000..4723787 --- /dev/null +++ b/tests/test_tenx_utils.py @@ -0,0 +1,54 @@ +from os.path import join, dirname + +from rnaseq_pipeline import SequencingFileType, get_fastq_filenames_for_10x_sequencing_layout +from rnaseq_pipeline.tenx_utils import read_sequencing_layout_from_10x_bam_header + +test_data_dir = join(dirname(__file__), 'data') + +def test(): + with open(join(test_data_dir, 'YY1R.bam-header.txt')) as f: + l = read_sequencing_layout_from_10x_bam_header(f) + assert len(l) == 3 + assert 's10_MissingLibrary_1_HG3T5BGX2' in l + assert 's10_MissingLibrary_1_HHJT3BGX2' in l + assert 's10_MissingLibrary_1_HYHJ7BGXY' in l + for lane_id, lane in l['s10_MissingLibrary_1_HG3T5BGX2'].items(): + assert lane == [SequencingFileType.I1, SequencingFileType.R1, SequencingFileType.R2] + assert get_fastq_filenames_for_10x_sequencing_layout(l) == [ + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HG3T5BGX2/bamtofastq_S1_L004_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HHJT3BGX2/bamtofastq_S1_L004_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L001_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L002_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L003_R2_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_I1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R1_001.fastq.gz', + 's10_MissingLibrary_1_HYHJ7BGXY/bamtofastq_S1_L004_R2_001.fastq.gz' + ] From 3428a5d3f42a5bdfa01e0c3d129d8df7b3014313 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 21 Oct 2025 11:02:12 -0700 Subject: [PATCH 25/45] Add a task to reorganize a split experiment --- rnaseq_pipeline/tasks.py | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 4976dcd..7f41253 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -1,9 +1,10 @@ import datetime import logging import os.path +import shutil import tempfile import uuid -from glob import glob +from glob import glob, iglob from os import unlink, makedirs, link, symlink from os.path import dirname, join, basename, splitext @@ -792,3 +793,29 @@ def _filename(self): def _retrieve_dataframe(self): from .gsheet import retrieve_spreadsheet return retrieve_spreadsheet(self.spreadsheet_id, self.sheet_name) + +class ReorganizeSplitExperiment(GemmaTaskMixin): + """Reorganize a Gemma dataset that was split.""" + + num_splits: int = luigi.IntParameter() + + def run(self): + dirs_to_relocate = [ + join(cfg.OUTPUT_DIR, 'data-trimmed'), + join(cfg.OUTPUT_DIR, cfg.DATAQCDIR), + join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, '*'), + join(cfg.OUTPUT_DIR, cfg.QUANTDIR, '*'), + join(cfg.OUTPUT_DIR, 'quantified-single-cell', '*') + ] + + for split_id in range(self.num_splits): + split_id = self.experiment_id + '.' + str(split_id + 1) + logger.info('Reorganizing data for %s.', split_id) + for sample in self._gemma_api.samples(split_id): + sample_id = sample['accession']['accession'] + for d in dirs_to_relocate: + for sample_file in iglob(join(d, self.experiment_id, sample_id)): + new_sample_file = join(dirname(dirname(sample_file)), split_id, sample_id) + logger.info('Moving %s to %s.', sample_file,new_sample_file) + os.makedirs(dirname(new_sample_file), exist_ok=True) + shutil.move(sample_file, new_sample_file) From 32139a5a6d56878e2e94df67f6802d0dd3c5f962 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 21 Oct 2025 11:02:50 -0700 Subject: [PATCH 26/45] Remove unused ALIGNQCDIR --- example.luigi.cfg | 1 - rnaseq_pipeline/config.py | 1 - 2 files changed, 2 deletions(-) diff --git a/example.luigi.cfg b/example.luigi.cfg index b9c8e96..6dbbfd6 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -48,7 +48,6 @@ METADATA=metadata DATA=data DATAQCDIR=data-qc ALIGNDIR=aligned -ALIGNQCDIR=aligned-qc QUANTDIR=quantified BATCHINFODIR=batch-info diff --git a/rnaseq_pipeline/config.py b/rnaseq_pipeline/config.py index c052c43..08087b9 100644 --- a/rnaseq_pipeline/config.py +++ b/rnaseq_pipeline/config.py @@ -15,7 +15,6 @@ class rnaseq_pipeline(luigi.Config): DATA: str = luigi.Parameter() DATAQCDIR: str = luigi.Parameter() ALIGNDIR: str = luigi.Parameter() - ALIGNQCDIR: str = luigi.Parameter() QUANTDIR: str = luigi.Parameter() BATCHINFODIR: str = luigi.Parameter() From 5fb0325efb2cd22fd0de9405d3bbab864672f3c0 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 21 Oct 2025 13:47:57 -0700 Subject: [PATCH 27/45] Rename output files of bamtofastq not ending in '_001.fastq.gz' --- rnaseq_pipeline/sources/sra.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 21d7220..cc4c9b0 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -9,6 +9,7 @@ import xml.etree.ElementTree as ET from dataclasses import dataclass from datetime import timedelta +from glob import glob from os.path import join, basename from typing import Optional, List @@ -579,6 +580,15 @@ def run(self): output_dir=self.output_dir, cpus=4, scheduler_extra_args=['--constraint', 'thrd64']) + + # The BAM header does not indicate the last digits in the filename + # rename _XXX.fastq.gz to _001.fastq.gz + for fastq_file in glob(join(self.output_dir, '*/*.fastq.gz')): + if not fastq_file.endswith('_001.fastq.gz'): + new_name = fastq_file.rsplit('_', maxsplit=1)[0] + '_001.fastq.gz' + logger.info('Renaming %s to %s.', fastq_file, new_name) + os.rename(fastq_file, new_name) + if not self.complete(): raise RuntimeError('Expected output files from bamtofastq were not produced:\n\t' + '\n\t'.join( f for rt in self.output() for f in rt.files)) From 5e8006a06b9d81fb4644deeda76ddff4680bc36e Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 21 Oct 2025 13:49:16 -0700 Subject: [PATCH 28/45] Check if read_types is provided when detecting layout --- rnaseq_pipeline/rnaseq_utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/rnaseq_utils.py b/rnaseq_pipeline/rnaseq_utils.py index 59ca01f..56ed00f 100644 --- a/rnaseq_pipeline/rnaseq_utils.py +++ b/rnaseq_pipeline/rnaseq_utils.py @@ -56,8 +56,10 @@ def detect_layout(run_id: str, filenames: Optional[list[str]], number_of_files = len(filenames) elif average_read_lengths: number_of_files = len(average_read_lengths) - else: + elif read_types: number_of_files = len(read_types) + else: + raise ValueError(f'No metadata is present to infer layout for {run_id}.') # assume single-end read if only one file is present if number_of_files == 1: From 8e3fbaa96803bc7ef36ad609e166ca7e26218184 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Wed, 22 Oct 2025 10:49:15 -0700 Subject: [PATCH 29/45] Rename wrapped tools config section --- example.luigi.cfg | 2 +- rnaseq_pipeline/wrapped_tools.py | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/example.luigi.cfg b/example.luigi.cfg index 6dbbfd6..2d86a2c 100644 --- a/example.luigi.cfg +++ b/example.luigi.cfg @@ -57,7 +57,7 @@ rsem_calculate_expression_bin=contrib/RSEM/rsem-calculate-expression SLACK_WEBHOOK_URL= -[rnaseq_pipeline.wrapped_tools.WrappedTools] +[rnaseq_pipeline.wrapped_tools] rsem_calculate_expression_bin=rsem-calculate-expression cellranger_bin=cellranger diff --git a/rnaseq_pipeline/wrapped_tools.py b/rnaseq_pipeline/wrapped_tools.py index d761a5e..2f1abaa 100644 --- a/rnaseq_pipeline/wrapped_tools.py +++ b/rnaseq_pipeline/wrapped_tools.py @@ -19,6 +19,10 @@ from luigi.contrib.external_program import ExternalProgramRunContext class WrappedToolsConfig(luigi.Config): + @classmethod + def get_task_family(cls): + return 'rnaseq_pipeline.wrapped_tools' + cellranger_bin: str = luigi.Parameter() rsem_calculate_expression_bin: str = luigi.Parameter() From cfd4a30b062d555a49881be3356b06ca1893baee Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Sun, 26 Oct 2025 08:31:38 -0700 Subject: [PATCH 30/45] More work --- pytest.ini | 3 +- rnaseq_pipeline/cli.py | 45 ++++++++++++++++--------- rnaseq_pipeline/config.py | 28 ++++++++------- rnaseq_pipeline/gemma.py | 44 +++++++++++++----------- rnaseq_pipeline/sources/arrayexpress.py | 4 +-- rnaseq_pipeline/sources/gemma.py | 4 +-- rnaseq_pipeline/sources/geo.py | 4 +-- rnaseq_pipeline/sources/local.py | 4 +-- rnaseq_pipeline/sources/sra.py | 35 ++++++++++++------- rnaseq_pipeline/tasks.py | 40 +++++++++++++++------- rnaseq_pipeline/webviewer/__init__.py | 4 +-- rnaseq_pipeline/wrapped_tools.py | 11 +++--- tests/test_sra.py | 12 ++++--- tests/test_tasks.py | 2 +- 14 files changed, 145 insertions(+), 95 deletions(-) diff --git a/pytest.ini b/pytest.ini index baad504..9a9039d 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,3 +1,4 @@ [pytest] +testpaths=tests log_cli=1 -log_cli_level=info \ No newline at end of file +log_cli_level=info diff --git a/rnaseq_pipeline/cli.py b/rnaseq_pipeline/cli.py index 2110529..8459530 100644 --- a/rnaseq_pipeline/cli.py +++ b/rnaseq_pipeline/cli.py @@ -5,9 +5,9 @@ import luigi import luigi.cmdline -import bioluigi.cli -from rnaseq_pipeline.tasks import SubmitExperimentToGemma, SubmitExperimentsFromGoogleSpreadsheetToGemma, SubmitExperimentBatchInfoToGemma +from rnaseq_pipeline.tasks import SubmitExperimentToGemma, SubmitExperimentsFromGoogleSpreadsheetToGemma, \ + SubmitExperimentBatchInfoToGemma @contextmanager def umask(umask): @@ -22,56 +22,69 @@ def umask(umask): def parse_octal(s): return int(s, 8) - def run_luigi_task(task, args): with umask(args.umask): luigi.build([task], workers=args.workers, detailed_summary=True, local_scheduler=args.local_scheduler) +def run(args): + with umask(0o002): + luigi.run(args) + def submit_experiment(argv): parser = argparse.ArgumentParser() parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma') parser.add_argument('--rerun', action='store_true', default=False, help='Rerun the experiment') parser.add_argument('--priority', type=int, default=100) - parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--umask', type=parse_octal, default='002', + help='Set a umask (defaults to 002 to make created files group-writable)') parser.add_argument('--workers', type=int, default=30, help='Number of workers to use (defaults to 30)') parser.add_argument('--local-scheduler', action='store_true', default=False) args = parser.parse_args(argv) - run_luigi_task(SubmitExperimentToGemma(experiment_id=args.experiment_id, rerun=args.rerun, priority=args.priority), args) + run_luigi_task(SubmitExperimentToGemma(experiment_id=args.experiment_id, rerun=args.rerun, priority=args.priority), + args) def submit_experiment_batch_info(argv): parser = argparse.ArgumentParser() parser.add_argument('--experiment-id', required=True, help='Experiment ID to submit to Gemma') parser.add_argument('--ignored-samples', nargs='+', default=[]) parser.add_argument('--rerun', action='store_true', default=False, help='Rerun the experiment') - parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--umask', type=parse_octal, default='002', + help='Set a umask (defaults to 002 to make created files group-writable)') parser.add_argument('--workers', type=int, default=30, help='Number of workers to use (defaults to 30)') parser.add_argument('--local-scheduler', action='store_true', default=False) args = parser.parse_args(argv) print(args.ignored_samples) - run_luigi_task(SubmitExperimentBatchInfoToGemma(experiment_id=args.experiment_id, ignored_samples=args.ignored_samples, rerun=args.rerun), args) + run_luigi_task( + SubmitExperimentBatchInfoToGemma(experiment_id=args.experiment_id, ignored_samples=args.ignored_samples, + rerun=args.rerun), args) def submit_experiments_from_gsheet(argv): parser = argparse.ArgumentParser() parser.add_argument('--spreadsheet-id', required=True, help='Spreadsheet ID') parser.add_argument('--sheet-name', required=True, help='Sheet name') - parser.add_argument('--umask', type=parse_octal, default='002', help='Set a umask (defaults to 002 to make created files group-writable)') + parser.add_argument('--umask', type=parse_octal, default='002', + help='Set a umask (defaults to 002 to make created files group-writable)') parser.add_argument('--workers', type=int, default=200, help='Number of workers to use (defaults to 200)') parser.add_argument('--ignore-priority', action='store_true', help='Ignore the priority column in the spreadsheet') parser.add_argument('--local-scheduler', action='store_true', default=False) args = parser.parse_args(argv) - run_luigi_task(SubmitExperimentsFromGoogleSpreadsheetToGemma(args.spreadsheet_id, args.sheet_name, ignore_priority=args.ignore_priority), args) + run_luigi_task(SubmitExperimentsFromGoogleSpreadsheetToGemma(args.spreadsheet_id, args.sheet_name, + ignore_priority=args.ignore_priority), args) def main(): if len(sys.argv) < 2: print('Usage: rnaseq-pipeline-cli ') - sys.exit(1) + return 1 command = sys.argv[1] - if command == 'submit-experiment': - sys.exit(submit_experiment(sys.argv[2:])) + if command == 'run': + return run(sys.argv[2:]) + elif command == 'submit-experiment': + return submit_experiment(sys.argv[2:]) elif command == 'submit-experiment-batch-info': - sys.exit(submit_experiment_batch_info(sys.argv[2:])) + return submit_experiment_batch_info(sys.argv[2:]) elif command == 'submit-experiments-from-gsheet': - sys.exit(submit_experiments_from_gsheet(sys.argv[2:])) + return submit_experiments_from_gsheet(sys.argv[2:]) else: - print(f'Unknown command {command}. Possible values are: submit-experiment, submit-experiment-batch-info, submit-experiments-from-gsheet.') - sys.exit(1) + print( + f'Unknown command {command}. Possible values are: submit-experiment, submit-experiment-batch-info, submit-experiments-from-gsheet.') + return 1 diff --git a/rnaseq_pipeline/config.py b/rnaseq_pipeline/config.py index 08087b9..554385e 100644 --- a/rnaseq_pipeline/config.py +++ b/rnaseq_pipeline/config.py @@ -3,23 +3,25 @@ import luigi # see luigi.cfg for details -class rnaseq_pipeline(luigi.Config): - task_namespace = '' +class Config(luigi.Config): + @classmethod + def get_task_family(cls): + return 'rnaseq_pipeline' GENOMES: str = luigi.Parameter() - OUTPUT_DIR: str = luigi.Parameter() - REFERENCES: str = luigi.Parameter() - SINGLE_CELL_REFERENCES: str = luigi.Parameter() - METADATA: str = luigi.Parameter() - DATA: str = luigi.Parameter() - DATAQCDIR: str = luigi.Parameter() - ALIGNDIR: str = luigi.Parameter() - QUANTDIR: str = luigi.Parameter() - BATCHINFODIR: str = luigi.Parameter() + OUTPUT_DIR: str = luigi.Parameter(default='genomes') + REFERENCES: str = luigi.Parameter(default='references') + SINGLE_CELL_REFERENCES: str = luigi.Parameter(default='references-single-cell') + METADATA: str = luigi.Parameter(default='metadata') + DATA: str = luigi.Parameter(default='data') + DATAQCDIR: str = luigi.Parameter(default='data-qc') + ALIGNDIR: str = luigi.Parameter(default='aligned') + QUANTDIR: str = luigi.Parameter(default='quantified') + BATCHINFODIR: str = luigi.Parameter(default='batch-info') - RSEM_DIR: str = luigi.Parameter() + RSEM_DIR: str = luigi.Parameter(default='contrib/RSEM') - rsem_calculate_expression_bin: str = luigi.Parameter() + rsem_calculate_expression_bin: str = luigi.Parameter(default='contrib/RSEM/rsem-calculate-expression') SLACK_WEBHOOK_URL: Optional[str] = luigi.OptionalParameter(default=None) diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py index 710ec5d..b6ce825 100644 --- a/rnaseq_pipeline/gemma.py +++ b/rnaseq_pipeline/gemma.py @@ -4,6 +4,7 @@ import subprocess from getpass import getpass from os.path import join +from typing import Optional import luigi import requests @@ -12,13 +13,16 @@ logger = logging.getLogger(__name__) -class gemma(luigi.Config): - task_namespace = 'rnaseq_pipeline' - baseurl: str = luigi.Parameter() - appdata_dir: str = luigi.Parameter() - cli_bin: str = luigi.Parameter() - cli_JAVA_HOME: str = luigi.Parameter() - cli_JAVA_OPTS: str = luigi.Parameter() +class GemmaConfig(luigi.Config): + @classmethod + def get_task_family(cls): + return 'rnaseq_pipeline.gemma' + + baseurl: str = luigi.Parameter(default='https://gemma.msl.ubc.ca', description='Base URL for Gemma') + appdata_dir: str = luigi.Parameter(description='Directory where Gemma data is stored') + cli_bin: str = luigi.Parameter(default='gemma-cli', description='Gemma CLI tool name') + cli_JAVA_HOME: Optional[str] = luigi.Parameter(default=None, description='Override $JAVA_HOME for the Gemma CLI') + cli_JAVA_OPTS: Optional[str] = luigi.Parameter(default=None, description='Override $JAVA_OPTS for the Gemma CLI') human_reference_id: str = luigi.Parameter() mouse_reference_id: str = luigi.Parameter() rat_reference_id: str = luigi.Parameter() @@ -26,7 +30,7 @@ class gemma(luigi.Config): mouse_single_cell_reference_id: str = luigi.Parameter() rat_single_cell_reference_id: str = luigi.Parameter() -cfg = gemma() +cfg = GemmaConfig() class GemmaApi: def __init__(self): @@ -103,17 +107,15 @@ def taxon(self): @property def reference_id(self): try: - return {'human': cfg.human_reference_id, 'mouse': cfg.mouse_reference_id, 'rat': cfg.rat_reference_id}[ - self.taxon] - except KeyError: - raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) - - @property - def single_cell_reference_id(self): - try: - return {'human': cfg.human_single_cell_reference_id, 'mouse': cfg.mouse_single_cell_reference_id, - 'rat': cfg.rat_single_cell_reference_id}[ + if self.assay_type == GemmaAssayType.BULK_RNA_SEQ: + return {'human': cfg.human_reference_id, 'mouse': cfg.mouse_reference_id, 'rat': cfg.rat_reference_id}[ self.taxon] + elif self.assay_type == GemmaAssayType.SINGLE_CELL_RNA_SEQ: + return {'human': cfg.human_single_cell_reference_id, 'mouse': cfg.mouse_single_cell_reference_id, + 'rat': cfg.rat_single_cell_reference_id}[ + self.taxon] + else: + raise NotImplementedError except KeyError: raise ValueError('Unsupported Gemma taxon {}.'.format(self.taxon)) @@ -179,8 +181,10 @@ class GemmaCliTask(GemmaTaskMixin, ExternalProgramTask): def program_environment(self): env = super().program_environment() - env['JAVA_HOME'] = cfg.cli_JAVA_HOME - env['JAVA_OPTS'] = cfg.cli_JAVA_OPTS + if cfg.cli_JAVA_HOME: + env['JAVA_HOME'] = cfg.cli_JAVA_HOME + if cfg.cli_JAVA_OPTS: + env['JAVA_OPTS'] = cfg.cli_JAVA_OPTS return env def program_args(self): diff --git a/rnaseq_pipeline/sources/arrayexpress.py b/rnaseq_pipeline/sources/arrayexpress.py index 65e0c4b..233bc88 100644 --- a/rnaseq_pipeline/sources/arrayexpress.py +++ b/rnaseq_pipeline/sources/arrayexpress.py @@ -9,12 +9,12 @@ from bioluigi.tasks.utils import TaskWithOutputMixin from luigi.task import WrapperTask -from ..config import rnaseq_pipeline +from ..config import Config from ..platforms import IlluminaPlatform from ..rnaseq_utils import detect_layout from ..targets import DownloadRunTarget -cfg = rnaseq_pipeline() +cfg = Config() @lru_cache() def retrieve_metadata(experiment_id): diff --git a/rnaseq_pipeline/sources/gemma.py b/rnaseq_pipeline/sources/gemma.py index 5edaf3a..ce278fd 100644 --- a/rnaseq_pipeline/sources/gemma.py +++ b/rnaseq_pipeline/sources/gemma.py @@ -5,12 +5,12 @@ from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask from .geo import DownloadGeoSample from .sra import DownloadSraExperiment -from ..config import rnaseq_pipeline +from ..config import Config from ..gemma import GemmaApi logger = logging.getLogger(__name__) -cfg = rnaseq_pipeline() +cfg = Config() class DownloadGemmaExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): """ diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py index 34ce143..e9f4b7a 100644 --- a/rnaseq_pipeline/sources/geo.py +++ b/rnaseq_pipeline/sources/geo.py @@ -22,13 +22,13 @@ from luigi.task import flatten from .sra import DownloadSraExperiment -from ..config import rnaseq_pipeline +from ..config import Config from ..miniml_utils import collect_geo_samples, collect_geo_samples_info from ..platforms import BgiPlatform, IlluminaPlatform from ..targets import ExpirableLocalTarget from ..utils import RerunnableTaskMixin -cfg = rnaseq_pipeline() +cfg = Config() logger = logging.getLogger(__name__) diff --git a/rnaseq_pipeline/sources/local.py b/rnaseq_pipeline/sources/local.py index d548eec..a432a30 100644 --- a/rnaseq_pipeline/sources/local.py +++ b/rnaseq_pipeline/sources/local.py @@ -4,10 +4,10 @@ import luigi from bioluigi.tasks.utils import TaskWithOutputMixin -from ..config import rnaseq_pipeline +from ..config import Config from ..platforms import IlluminaPlatform, BgiPlatform, IlluminaNexteraPlatform, TaskWithPlatformMixin -cfg = rnaseq_pipeline() +cfg = Config() class DownloadLocalSample(TaskWithPlatformMixin, luigi.Task): """ diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index cc4c9b0..74d746a 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -20,7 +20,7 @@ from bioluigi.tasks.utils import TaskWithMetadataMixin, DynamicTaskWithOutputMixin, DynamicWrapperTask from luigi.util import requires -from ..config import rnaseq_pipeline +from ..config import Config from ..platforms import IlluminaPlatform from ..rnaseq_utils import SequencingFileType, detect_layout from ..targets import ExpirableLocalTarget, DownloadRunTarget @@ -28,18 +28,23 @@ get_fastq_filename from ..utils import remove_task_output, RerunnableTaskMixin -cfg = rnaseq_pipeline() +cfg = Config() logger = logging.getLogger(__name__) -class sra(luigi.Config): - task_namespace = 'rnaseq_pipeline.sources' - ncbi_public_dir: str = luigi.Parameter() - samtools_bin: str = luigi.Parameter() - bamtofastq_bin: str = luigi.Parameter() - bam_headers_cache_dir: str = luigi.Parameter() +class SraConfig(luigi.Config): + @classmethod + def get_task_family(cls): + return 'rnaseq_pipeline.sources.sra' -sra_config = sra() + ncbi_public_dir: str = luigi.Parameter(description='Path to the NCBI public directory.') + curl_bin: str = luigi.Parameter(default='curl') + samtools_bin: str = luigi.Parameter(default='samtools') + bamtofastq_bin: str = luigi.Parameter(default='bamtofastq') + bam_headers_cache_dir: str = luigi.Parameter(default='bam_headers', + description='Directory where to store BAM file headers downloaded from SRA files.') + +sra_config = SraConfig() # columns to use when a runinfo file lacks a header SRA_RUNINFO_COLUMNS = ['Run', 'ReleaseDate', 'LoadDate', 'spots', 'bases', 'spots_with_mates', 'avgLength', 'size_MB', @@ -189,6 +194,13 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: number_of_spots = int(statistics.attrib['nreads']) if statistics.attrib['nreads'] != 'variable' else None reads = sorted(statistics.findall('Read'), key=lambda r: int(r.attrib['index'])) spot_read_lengths = [float(r.attrib['average']) for r in reads] + # check for zero-length reads, perform traversal in reverse order to preserve indices + for i, srl in reversed(list(enumerate(spot_read_lengths))): + if srl == 0: + logger.warning('%s: Empty read for position %d in spot, will ignore it.', srr, i + 1) + number_of_spots -= 1 + reads.pop(i) + spot_read_lengths.pop(i) else: logger.warning( '%s: No spot statistics found, cannot use the average read lengths to determine the order of the FASTQ files.', @@ -455,7 +467,7 @@ def read_bam_header(srr, filename, url): with open(bam_header_file, 'w') as f: # FIXME: use requests # res = requests.get(bam_file.attrib['url'], stream=True) - with subprocess.Popen(['curl', url], stdout=subprocess.PIPE, + with subprocess.Popen([sra_config.curl_bin, url], stdout=subprocess.PIPE, stderr=subprocess.DEVNULL) as curl_proc: try: subprocess.run([sra_config.samtools_bin, 'head'], @@ -512,7 +524,6 @@ def run(self): yield sratoolkit.FastqDump(input_file=self.input().path, output_dir=self.output_dir, split='files', - number_of_reads_per_spot=len(self.layout), metadata=self.metadata) if not self.complete(): raise RuntimeError( @@ -564,7 +575,7 @@ class DumpBamRun(TaskWithMetadataMixin, luigi.Task): _sequencing_layout = None @property - def sequencing_layout(self) -> dict[str, dict[int, list[SequencingFileType]]]: + def sequencing_layout(self) -> dict[str, dict[int, list[SequencingFileType]]]: if self._sequencing_layout is None: with open(read_bam_header(self.srr, self.filename, self.file_url), 'r') as f: self._sequencing_layout = read_sequencing_layout_from_10x_bam_header(f) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 7f41253..01a8b7d 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -21,8 +21,8 @@ from bioluigi.tasks.cellranger import CellRangerCount from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask from bioluigi.tasks.utils import TaskWithOutputMixin -from rnaseq_pipeline.config import rnaseq_pipeline -from .gemma import GemmaAssayType, GemmaTaskMixin, gemma +from rnaseq_pipeline.config import Config +from .gemma import GemmaAssayType, GemmaTaskMixin, GemmaConfig from .gemma import GemmaCliTask from .sources.arrayexpress import DownloadArrayExpressSample, DownloadArrayExpressExperiment from .sources.gemma import DownloadGemmaExperiment @@ -39,8 +39,8 @@ logger = logging.getLogger(__name__) -cfg = rnaseq_pipeline() -gemma_cfg = gemma() +cfg = Config() +gemma_cfg = GemmaConfig() class DownloadSample(TaskWithOutputMixin, luigi.WrapperTask): """ @@ -326,10 +326,10 @@ def program_args(self): reverse_reads = [] for run in runs: if len(run) == 2: - forward_reads.append(run[0]) - reverse_reads.append(run[1]) + forward_reads.append(run[0].path) + reverse_reads.append(run[1].path) elif len(run) == 1: - forward_reads.append(run[0]) + forward_reads.append(run[0].path) else: raise NotImplementedError("Only single or paired-end sequencing is supported.") @@ -400,11 +400,19 @@ def run(self): search_dirs.update(dirname(out.path) for out in flatten(qc_sample_dirs)), search_dirs.update(dirname(out.path) for out in flatten(align_sample_dirs)) self.output().makedirs() - sample_names_file = join(dirname(self.output().path), 'sample_names.tsv') + # we used to write the sample_names.tsv file inside the directory, but that is not working anymore since writing + # MultiQC report now uses atomic write + sample_names_file = join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id + '.sample_names.tsv') with open(sample_names_file, 'w') as out: + for sample_trim_dirs in trim_sample_dirs: + for lane_trim in sample_trim_dirs: + run_id = '___'.join(basename(lt.path).removesuffix('.fastq.gz') + for lt in lane_trim) + sample_id = basename(dirname(dirname(lane_trim[0].path))) + out.write(f'{run_id}\t{sample_id}_{run_id}\n') for lane_qc in flatten(qc_sample_dirs): run_id = basename(lane_qc.path).removesuffix('_fastqc.html') - sample_id = basename(dirname(lane_qc.path)) + sample_id = basename(dirname(dirname(dirname(lane_qc.path)))) out.write(f'{run_id}\t{sample_id}_{run_id}\n') yield multiqc.GenerateReport(input_dirs=search_dirs, output_dir=dirname(self.output().path), @@ -546,9 +554,15 @@ def run(self): sample_names_file = join(cfg.OUTPUT_DIR, 'report', self.reference_id, self.experiment_id + '.sample_names.tsv') os.makedirs(dirname(sample_names_file), exist_ok=True) with open(sample_names_file, 'w') as out: + for sample_trim_dirs in trim_sample_dirs: + for lane_trim in sample_trim_dirs: + run_id = '___'.join(basename(lt.path).removesuffix('.fastq.gz') + for lt in lane_trim) + sample_id = basename(dirname(dirname(lane_trim[0].path))) + out.write(f'{run_id}\t{sample_id}_{run_id}\n') for lane_qc in flatten(qc_sample_dirs): run_id = basename(lane_qc.path).removesuffix('_fastqc.html') - sample_id = basename(dirname(lane_qc.path)) + sample_id = basename(dirname(dirname(dirname(lane_qc.path)))) out.write(f'{run_id}\t{sample_id}_{run_id}\n') yield multiqc.GenerateReport(input_dirs=search_dirs, @@ -599,7 +613,7 @@ class SubmitSingleCellExperimentDataToGemma(GemmaCliTask): def requires(self): return AlignSingleCellExperiment(experiment_id=self.experiment_id, - reference_id=self.single_cell_reference_id, + reference_id=self.reference_id, source='gemma') def subcommand_args(self): @@ -683,7 +697,7 @@ def requires(self): rerun=self.rerun) elif self.assay_type == GemmaAssayType.SINGLE_CELL_RNA_SEQ: return GenerateReportForSingleCellExperiment(self.experiment_id, - reference_id=self.single_cell_reference_id, + reference_id=self.reference_id, source='gemma', rerun=self.rerun) else: @@ -816,6 +830,6 @@ def run(self): for d in dirs_to_relocate: for sample_file in iglob(join(d, self.experiment_id, sample_id)): new_sample_file = join(dirname(dirname(sample_file)), split_id, sample_id) - logger.info('Moving %s to %s.', sample_file,new_sample_file) + logger.info('Moving %s to %s.', sample_file, new_sample_file) os.makedirs(dirname(new_sample_file), exist_ok=True) shutil.move(sample_file, new_sample_file) diff --git a/rnaseq_pipeline/webviewer/__init__.py b/rnaseq_pipeline/webviewer/__init__.py index 2c972f5..c54bda1 100644 --- a/rnaseq_pipeline/webviewer/__init__.py +++ b/rnaseq_pipeline/webviewer/__init__.py @@ -6,14 +6,14 @@ import pandas as pd from flask import Flask, send_file, render_template, abort -from rnaseq_pipeline.config import rnaseq_pipeline +from rnaseq_pipeline.config import Config from rnaseq_pipeline.gemma import GemmaTaskMixin from rnaseq_pipeline.tasks import GenerateReportForExperiment, CountExperiment, SubmitExperimentDataToGemma, \ SubmitExperimentBatchInfoToGemma app = Flask('rnaseq_pipeline.webviewer') -cfg = rnaseq_pipeline() +cfg = Config() references = ['hg38_ncbi', 'mm10_ncbi', 'm6_ncbi'] diff --git a/rnaseq_pipeline/wrapped_tools.py b/rnaseq_pipeline/wrapped_tools.py index 2f1abaa..95bfe0a 100644 --- a/rnaseq_pipeline/wrapped_tools.py +++ b/rnaseq_pipeline/wrapped_tools.py @@ -74,19 +74,20 @@ def subprocess_run(args, **kwargs): def rsem_calculate_expression_wrapper(): """Wrapper script for RSEM that copies the reference to a local temporary directory.""" args = sys.argv.copy() - args[0] = cfg.rsem_calculate_expression_bin + # execv expects an absolute path + args[0] = shutil.which(cfg.rsem_calculate_expression_bin) if len(args) > 2 and os.path.isdir(args[-2]): # copy the reference to local scratch ref_dir = args[-2] new_dir, lockfile = copy_directory_to_local_scratch(ref_dir) args[-2] = new_dir with lockf(lockfile) as f: - print('Final command: ' + ' '.join(args)) + print('Final command: ' + ' '.join(args), flush=True) os.set_inheritable(f.fileno(), True) - os.execv(args[0], args[1:]) + os.execv(args[0], args) else: - print('Final command: ' + ' '.join(args)) - os.execv(args[0], args[1:]) + print('Final command: ' + ' '.join(args), flush=True) + os.execv(args[0], args) def cellranger_wrapper(): args = sys.argv.copy() diff --git a/tests/test_sra.py b/tests/test_sra.py index 956477e..d374d03 100644 --- a/tests/test_sra.py +++ b/tests/test_sra.py @@ -189,8 +189,7 @@ def test_read_xml_metadata_GSE104493(): """This dataset has I1 reads with zero length""" meta = read_xml_metadata(join(test_data_dir, 'GSE104493.xml')) for run in meta: - assert run.layout == [I1, R1] - assert run.average_read_lengths[0] == 0.0 + assert run.layout == [R1] def test_read_xml_metadata_GSE125536(): """This dataset does not have SRAFile entries, but it has fastq-load.py inputs which can be used as a fallback.""" @@ -202,7 +201,7 @@ def test_read_xml_metadata_GSE128117(): """This dataset has a sample with 3 reads (R1, R2, R3) and an index (I1).""" meta = read_xml_metadata(join(test_data_dir, 'GSE128117.xml')) for run in meta: - assert run.layout == [R1, I1] + assert run.layout == [R1] def test_read_xml_metadata_SRX26261721(): meta = read_xml_metadata(join(test_data_dir, 'SRX26261721.xml')) @@ -283,7 +282,7 @@ def test_SRX17676975(): def test_GSE271769(): runs = read_xml_metadata(join(test_data_dir, 'GSE271769.xml')) - assert len(runs) == 9 + assert len(runs) == 16 task = DownloadSraExperiment(srx='SRX25247848') task.run() @@ -296,6 +295,11 @@ def test_SRX26528278(): runs = read_xml_metadata(join(test_data_dir, 'SRX26528278.xml')) assert len(runs) == 1 +def test_SRR14827398(): + runs = read_xml_metadata(join(test_data_dir, 'SRR14827398.xml')) + for run in runs: + assert run.layout == [R1] + def test_read_runinfo(): meta = read_runinfo(join(test_data_dir, 'SRX26261721.runinfo')) assert len(meta) == 2 diff --git a/tests/test_tasks.py b/tests/test_tasks.py index 7b41fd1..2494d85 100644 --- a/tests/test_tasks.py +++ b/tests/test_tasks.py @@ -4,7 +4,7 @@ from rnaseq_pipeline.sources.geo import match_geo_platform from rnaseq_pipeline.tasks import * -cfg = rnaseq_pipeline() +cfg = Config() def test_illumina_platform(): plt = match_geo_platform('GPL29601') From ba16abce92b3b8bfe9080ada4104e62d8cabe3f8 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Sun, 26 Oct 2025 08:54:29 -0700 Subject: [PATCH 31/45] Add missing test data --- tests/data/SRR14827398.xml | 215 +++++++++++++++++++++++++++++++++++++ tests/data/SRX17676975.xml | 187 ++++++++++++++++++++++++++++++++ 2 files changed, 402 insertions(+) create mode 100644 tests/data/SRR14827398.xml create mode 100644 tests/data/SRX17676975.xml diff --git a/tests/data/SRR14827398.xml b/tests/data/SRR14827398.xml new file mode 100644 index 0000000..c362262 --- /dev/null +++ b/tests/data/SRR14827398.xml @@ -0,0 +1,215 @@ + + + + + + + SRX11156992 + + GSM5387188: WT_4_bulkRNA; Mus musculus; RNA-Seq + + + SRP324250 + + + + + + + SRS9218497 + GSM5387188 + + + + RNA-Seq + TRANSCRIPTOMIC + cDNA + + + + Mice brain hemispheres (without cerebellum and olfactory bulb) were enzymatically and mechanically dissociated using Miltenyi adult brain dissociation kit under 37 °C for 30 min. Dissociated tissue suspensions were purified with Miltenyi RBC lysis and debris removal reagents. The acquired single-cell suspensions were stained by CD11b beads and passed through the Miltenyi magnetic field for microglia cell enrichment. Further, total RNA was extracted from sorted microglia cells using the RNeasy Micro kit (Qiagen). mRNA libraries were prepared using illumina TruSeq protocol and sequenced by illumina HiSeq 4000 + + + + + Illumina HiSeq 4000 + + + + + + gds + 305387188 + + + + + + + GEO Accession + GSM5387188 + + + + + + SRA1245604 + GEO: GSE178296 + + + + NCBI + + + Geo + Curators + + + + + + SRP324250 + PRJNA738380 + GSE178296 + + + Transcriptome profiling of mouse brain microglia in Cnp null mice with 5xFAD background + + Alzheimer's disease (AD) is the most common form of dementia and neurodegenerative disease with increasing prevalence due to longer lifespan in the human population. Why aging constitutes the greatest risk factor for development of AD, however, remains poorly understood. Aging markedly affects oligodendrocytes and the structural integrity of their myelin sheaths which also causes secondary tissue inflammation. We propose a mechanistic link between aging-associated myelin dysfunction and the deposition of Amyloid-ß (Aß) as primary neuropathological hallmark of early AD and hypothesized that breakdown of myelin - especially in cortical regions – is an upstream driver of amyloid deposition in AD. Here, we show that in transgenic mouse models of AD, genetically induced myelin defects by Cnp or Plp1 depletion, as well as direct demyelination are potent drivers of amyloid deposition in vivo as shown by light sheet microscopy imaging. At transcriptomic level, bulk and single-cell RNA sequencing revealed successfully induced disease-associated-microglia (DAM)-like phenotypes in Cnp-/- animals. These activated microglia, however, are primarily engaged with myelin seemingly preventing the protective reactions of the microglia pool to Aß plaques. Our work, therefore, identifies myelin aging as a previously overlooked risk factor for AD and makes the case for myelin health-directed therapies in AD. Overall design: Microglia cells from 6-month-old mouse brain hemispheres were isolated using the MACS sorting system and subjected to 50 bp single-end mRNA sequencing. Each genotype has n=4 replicates, in total 4 genotypes were included for experiment (WT, Cnp-/-, 5xFAD, Cnp-/-x5xFAD). + GSE178296 + + + + + pubmed + 37258678 + + + + + + parent_bioproject + PRJNA738456 + + + + + + SRS9218497 + SAMN19728218 + GSM5387188 + + WT_4_bulkRNA + + 10090 + Mus musculus + + + + + bioproject + 738380 + + + + + + + source_name + Brain + + + strain + C57BL6/J + + + age + 6-month + + + genotype + WT + + + cell type + Microglia + + + tissue + Brain + + + mouse model + Alzheimer's disease (AD) + + + + + + + SRS9218497 + SAMN19728218 + GSM5387188 + + + + + + + SRR14827398 + GSM5387188_r1 + + + + + + SRS9218497 + SAMN19728218 + GSM5387188 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/data/SRX17676975.xml b/tests/data/SRX17676975.xml new file mode 100644 index 0000000..9f69ec5 --- /dev/null +++ b/tests/data/SRX17676975.xml @@ -0,0 +1,187 @@ + + + + + + + SRX17676975 + GSM6597361_r1 + + GSM6597361: F15; Homo sapiens; RNA-Seq + + + SRP398750 + PRJNA883411 + + + + + + + SRS15208996 + GSM6597361 + + + + GSM6597361 + RNA-Seq + TRANSCRIPTOMIC SINGLE CELL + cDNA + + + + Chromium Single Cell 3' Reagent Kits v2 and v3.1 + + + + + Illumina NovaSeq 6000 + + + + + + SRA1504501 + SUB12094265 + + + + McGill Group for Suicide Studies, Psychiatry, McGill University + +
+ 6875 Boulevard LaSalle + Montreal + Quebec + Canada +
+ + Gustavo + Turecki + + + + + + SRP398750 + PRJNA883411 + GSE213982 + + + Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq] + + We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in female MDD subjects who died by suicide and in female control subjects to identify cell-type specific differentially expressed genes. We further re-processed in parallel a previously generated snRNA-seq dataset in males with or without MDD to generate comparable differential expression results and compare the cell-type specific MDD-associated differences between the sexes. Overall design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 18 control subjects and 20 MDD cases who died by suicide. All subjects were female. We performed unsupervised clustering and pseudobulk differential gene expression was performed between cases and controls for each cluster and each broad brain cell type. The library preparation was performed with the Chromium Single Cell 3' Reagent Kits v3.1 or v2. Paired-end sequencing was performed on the Illumina NovaSeq 6000 or with BGI DNBSeq. FASTQ files were produced with Cellranger v3.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v5.1.0 count. Additionally, FASTQ files previously produced from a male cohort (GSE144136) were realigned and recounted, and raw count data from both sexes, which were input into differential expression analysis, along with the cell type annotations are included in the counts matrix provided. + GSE213982 + + + + + pubmed + 37217515 + + + + + + + SRS15208996 + SAMN30965500 + GSM6597361 + + F15 + + 9606 + Homo sapiens + + + + + bioproject + 883411 + + + + + + + source_name + Brain BA9 dlPFC + + + tissue + Brain BA9 dlPFC + + + Sex + female + + + group + Case + + + + + + + SRS15208996 + SAMN30965500 + GSM6597361 + + + + + + + SRR21678804 + GSM6597361_r1 + + + + GSM6597361_r1 + + + + + + SRS15208996 + SAMN30965500 + GSM6597361 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + From 31f87bdd38959bbdd4c3bc64eab9e03bf3d1d8d6 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 27 Oct 2025 12:00:51 -0700 Subject: [PATCH 32/45] Make it possible to delete an entire run directory instead of individual files --- rnaseq_pipeline/sources/sra.py | 13 +++++++++---- rnaseq_pipeline/targets.py | 33 ++++++++++++++++++++++++++------- 2 files changed, 35 insertions(+), 11 deletions(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 74d746a..7f3f26b 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -526,12 +526,16 @@ def run(self): split='files', metadata=self.metadata) if not self.complete(): + files = '\n\t'.join(glob(join(self.output_dir, '*.fastq.gz'))) raise RuntimeError( - f'{repr(self)} was not completed after successful fastq-dump execution; are the output files respecting the following layout: {self.layout}?') + f'{repr(self)} was not completed after successful fastq-dump execution; are the output files respecting the following layout: {self.layout}?\n\t{files}') def output(self): - return DownloadRunTarget(self.srr, [join(self.output_dir, self.srr + '_' + str(i + 1) + '.fastq.gz') for i in - range(len(self.layout))], self.layout) + return DownloadRunTarget(run_id=self.srr, + files=[join(self.output_dir, self.srr + '_' + str(i + 1) + '.fastq.gz') for i in + range(len(self.layout))], + layout=self.layout, + output_dir=self.output_dir) class EmptyRunInfoError(Exception): pass @@ -608,7 +612,8 @@ def output(self): return [DownloadRunTarget(run_id=f'{self.srr}_{flowcell_id}_L{lane_id:03}', files=[join(self.output_dir, get_fastq_filename(flowcell_id, lane_id, read_type)) for read_type in lane], - layout=self.layout) + layout=self.layout, + output_dir=self.output_dir) for flowcell_id, flowcell in self.sequencing_layout.items() for lane_id, lane in flowcell.items()] diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index 3a4c175..9af0746 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -1,7 +1,9 @@ import logging +import shutil from datetime import timedelta from os.path import join, exists, getctime, getmtime from time import time +from typing import Optional import luigi @@ -92,28 +94,45 @@ class DownloadRunTarget(luigi.Target): run_id: str files: list[str] layout: list[str] + output_dir: Optional[str] _targets: list[luigi.LocalTarget] - def __init__(self, run_id, files, layout): + def __init__(self, run_id, files, layout, output_dir=None): + """ + :param run_id: A run identifier + :param files: The output files of a run (e.g. R1.fastq.gz, R2.fastq.gz) + :param layout: The layout of the files (e.g. R1, R2, L1, L2, but also R3, R4, etc.) + :param output_dir: Directory in which all the files from the run are organized. If this is specified, remove() + will remove the directory instead of removing each target individually. + """ if len(files) != len(layout): raise ValueError('The number of files must match the layout.') self.run_id = run_id self.files = files self.layout = layout + self.output_dir = output_dir self._targets = [luigi.LocalTarget(f) for f in files] def exists(self): return all(t.exists() for t in self._targets) def remove(self): - for t in self._targets: - if t.exists(): + if self.output_dir: + if os.path.exists(self.output_dir): try: - t.remove() - logger.info('Removed %s.', repr(t)) - except: - logger.exception('Failed to remove %s.', repr(t)) + shutil.rmtree(self.output_dir) + logger.info('Removed %s.', self.output_dir) + except OSError: + logger.exception('Failed to remove %s.', self.output_dir) + else: + for t in self._targets: + if t.exists(): + try: + t.remove() + logger.info('Removed %s.', repr(t)) + except OSError: + logger.exception('Failed to remove %s.', repr(t)) def __repr__(self): return f"DownloadRunTarget(run_id={self.run_id}, files={self.files}, layout={'|'.join(self.layout)})" From bd43c52b15fc34e4e30bf2dfa05ae224f8ee1085 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 27 Oct 2025 12:01:41 -0700 Subject: [PATCH 33/45] sra: Include the SRA run identifier when dumping FASTQ files from a BAM --- rnaseq_pipeline/sources/sra.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index 7f3f26b..f0528f2 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -587,8 +587,7 @@ def sequencing_layout(self) -> dict[str, dict[int, list[SequencingFileType]]]: @property def output_dir(self): - # TODO: include the SRR identifier in the directory structure - return join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx) + return join(cfg.OUTPUT_DIR, cfg.DATA, 'sra', self.srx, self.srr) def run(self): yield cellranger.BamToFastq(input_file=self.input().path, From f84c3b1fa03cf96b05d831e29a9280cafb4a7c38 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 27 Oct 2025 12:59:19 -0700 Subject: [PATCH 34/45] Reduce the amount of configuration needed for the pipeline Add a minimal configuration for tests and provide a mock for gemma-cli. --- .github/workflows/build.yml | 2 +- rnaseq_pipeline/config.py | 5 +++-- rnaseq_pipeline/targets.py | 24 +++++++++++++++--------- rnaseq_pipeline/tasks.py | 4 ++-- rnaseq_pipeline/wrapped_tools.py | 4 ++-- tests/gemma-cli-mock | 0 tests/luigi.cfg | 21 +++++++++++++++++++++ 7 files changed, 44 insertions(+), 16 deletions(-) create mode 100755 tests/gemma-cli-mock create mode 100644 tests/luigi.cfg diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 70c8928..1d2e46a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -25,7 +25,7 @@ jobs: make -C scripts - name: Configure the pipeline run: | - cp example.luigi.cfg luigi.cfg + cp tests/luigi.cfg ./ - name: Test with pytest run: | conda install pytest diff --git a/rnaseq_pipeline/config.py b/rnaseq_pipeline/config.py index 554385e..d0f354f 100644 --- a/rnaseq_pipeline/config.py +++ b/rnaseq_pipeline/config.py @@ -8,9 +8,9 @@ class Config(luigi.Config): def get_task_family(cls): return 'rnaseq_pipeline' - GENOMES: str = luigi.Parameter() + OUTPUT_DIR: str = luigi.Parameter(default='pipeline-output') - OUTPUT_DIR: str = luigi.Parameter(default='genomes') + GENOMES: str = luigi.Parameter(default='genomes') REFERENCES: str = luigi.Parameter(default='references') SINGLE_CELL_REFERENCES: str = luigi.Parameter(default='references-single-cell') METADATA: str = luigi.Parameter(default='metadata') @@ -18,6 +18,7 @@ def get_task_family(cls): DATAQCDIR: str = luigi.Parameter(default='data-qc') ALIGNDIR: str = luigi.Parameter(default='aligned') QUANTDIR: str = luigi.Parameter(default='quantified') + QUANT_SINGLE_CELL_DIR: str = luigi.Parameter(default='quantified-single-cell') BATCHINFODIR: str = luigi.Parameter(default='batch-info') RSEM_DIR: str = luigi.Parameter(default='contrib/RSEM') diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index 9af0746..980033b 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -45,7 +45,7 @@ def exists(self): for platform in self._gemma_api.platforms(self.dataset_short_name)) def __repr__(self): - return 'GemmaDatasetPlatform(dataset_short_name={}, platform={})'.format(self.dataset_short_name, self.platform) + return f'GemmaDatasetPlatform(dataset_short_name={self.dataset_short_name}, platform={self.platform})' class GemmaDatasetHasBatch(luigi.Target): """ @@ -72,24 +72,30 @@ class ExpirableLocalTarget(luigi.LocalTarget): `use_mtime` parameter to use the modification time instead. """ - def __init__(self, path, ttl, use_mtime=False, format=None): - super().__init__(path, format=format) + ttl: timedelta + use_mtime: bool + + def __init__(self, path, ttl, use_mtime=False, **kwargs): + super().__init__(path, **kwargs) if not isinstance(ttl, timedelta): - self._ttl = timedelta(seconds=ttl) + self.ttl = timedelta(seconds=ttl) else: - self._ttl = ttl - self._use_mtime = use_mtime + self.ttl = ttl + self.use_mtime = use_mtime def is_stale(self): try: - creation_time = getmtime(self.path) if self._use_mtime else getctime(self.path) + creation_time = getmtime(self.path) if self.use_mtime else getctime(self.path) except OSError: return False # file is missing, assume non-stale - return creation_time + self._ttl.total_seconds() < time() + return creation_time + self.ttl.total_seconds() < time() def exists(self): return super().exists() and not self.is_stale() + def __repr__(self): + return f'ExpirableLocalTarget(path={self.path}, format={self.format}, fs={self.fs}, ttl={self.ttl}, use_mtime={self.use_mtime})' + class DownloadRunTarget(luigi.Target): run_id: str files: list[str] @@ -119,7 +125,7 @@ def exists(self): def remove(self): if self.output_dir: - if os.path.exists(self.output_dir): + if exists(self.output_dir): try: shutil.rmtree(self.output_dir) logger.info('Removed %s.', self.output_dir) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 01a8b7d..df16e5c 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -505,7 +505,7 @@ def run(self): def output(self): return luigi.LocalTarget( - join(cfg.OUTPUT_DIR, 'quantified-single-cell', self.reference_id, self.experiment_id, self.sample_id)) + join(cfg.OUTPUT_DIR, cfg.QUANT_SINGLE_CELL_DIR, self.reference_id, self.experiment_id, self.sample_id)) @requires(DownloadExperiment) class OrganizeSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): @@ -819,7 +819,7 @@ def run(self): join(cfg.OUTPUT_DIR, cfg.DATAQCDIR), join(cfg.OUTPUT_DIR, cfg.ALIGNDIR, '*'), join(cfg.OUTPUT_DIR, cfg.QUANTDIR, '*'), - join(cfg.OUTPUT_DIR, 'quantified-single-cell', '*') + join(cfg.OUTPUT_DIR, cfg.QUANT_SINGLE_CELL_DIR, '*') ] for split_id in range(self.num_splits): diff --git a/rnaseq_pipeline/wrapped_tools.py b/rnaseq_pipeline/wrapped_tools.py index 95bfe0a..de11505 100644 --- a/rnaseq_pipeline/wrapped_tools.py +++ b/rnaseq_pipeline/wrapped_tools.py @@ -23,8 +23,8 @@ class WrappedToolsConfig(luigi.Config): def get_task_family(cls): return 'rnaseq_pipeline.wrapped_tools' - cellranger_bin: str = luigi.Parameter() - rsem_calculate_expression_bin: str = luigi.Parameter() + cellranger_bin: str = luigi.Parameter(default='cellranger') + rsem_calculate_expression_bin: str = luigi.Parameter(default='contrib/RSEM/rsem-calculate-expression') cfg = WrappedToolsConfig() diff --git a/tests/gemma-cli-mock b/tests/gemma-cli-mock new file mode 100755 index 0000000..e69de29 diff --git a/tests/luigi.cfg b/tests/luigi.cfg new file mode 100644 index 0000000..41dc269 --- /dev/null +++ b/tests/luigi.cfg @@ -0,0 +1,21 @@ +[core] +autoload_range=true + +[rnaseq_pipeline.sources.sra] +# location where tools like prefetch and fastq-dump will store downloaded SRA files +# you can get this value with vdb-config -p +ncbi_public_dir=/tmp/ncbi/public + +[rnaseq_pipeline.gemma] +cli_bin=gemma-cli-mock +# values for $JAVA_HOME and $JAVA_OPTS environment variables +cli_JAVA_HOME= +cli_JAVA_OPTS= +baseurl=https://gemma.msl.ubc.ca +appdata_dir=/tmp/gemmaData +human_reference_id=hg38_ncbi +mouse_reference_id=mm10_ncbi +rat_reference_id=rn7_ncbi +human_single_cell_reference_id=refdata-gex-GRCh38-2024-A +mouse_single_cell_reference_id=refdata-gex-GRCm39-2024-A +rat_single_cell_reference_id=refdata-gex-mRatBN7-2-2024-A From 04af7e21fc13db1113bc240425608c86291ea687 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 27 Oct 2025 14:43:32 -0700 Subject: [PATCH 35/45] gemma: Add targets for specific QTs existing and use those as target for submitting data --- rnaseq_pipeline/gemma.py | 3 +++ rnaseq_pipeline/targets.py | 39 +++++++++++++++++++++++++++----------- rnaseq_pipeline/tasks.py | 11 ++++++----- tests/gemma-cli-mock | 1 + tests/test_targets.py | 16 ++++++++++++---- 5 files changed, 50 insertions(+), 20 deletions(-) diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py index b6ce825..c9affa6 100644 --- a/rnaseq_pipeline/gemma.py +++ b/rnaseq_pipeline/gemma.py @@ -68,6 +68,9 @@ def samples(self, experiment_id): def platforms(self, experiment_id): return self._query_api(join('datasets', experiment_id, 'platforms')) + def quantitation_types(self, experiment_id): + return self._query_api(join('datasets', experiment_id, 'quantitationTypes')) + class GemmaTaskMixin(luigi.Task): experiment_id = luigi.Parameter() diff --git a/rnaseq_pipeline/targets.py b/rnaseq_pipeline/targets.py index 980033b..ac95e52 100644 --- a/rnaseq_pipeline/targets.py +++ b/rnaseq_pipeline/targets.py @@ -1,3 +1,4 @@ +import enum import logging import shutil from datetime import timedelta @@ -29,23 +30,39 @@ def exists(self): return all(exists(self.prefix + '.' + ext) for ext in exts) -class GemmaDatasetPlatform(luigi.Target): - """ - Represents a platform associated to a Gemma dataset. - """ +class GemmaDataVectorType(enum.StrEnum): + """Data vector types in Gemma""" + RAW = 'ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector' + SINGLE_CELL = 'ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector' + PROCESSED = 'ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector' - def __init__(self, dataset_short_name, platform): - self.dataset_short_name = dataset_short_name - self.platform = platform +class GemmaDatasetQuantitationType(luigi.Target): + """Represents a quantitation type associated to a Gemma dataset.""" + + def __init__(self, + dataset: int | str, + quantitation_type: Optional[int | str] = None, + vector_type: Optional[GemmaDataVectorType] = None): + """ + :param dataset: The dataset identifier to lookup (either ID or short name) + :param quantitation_type: The identifier of the quantitation type (either name or ID) or the preferred one of + set to None. + :param vector_type: The type of vector to consider, or any if set to None. + """ + self.dataset = dataset + self.quantitation_type = quantitation_type + self.vector_type = vector_type self._gemma_api = GemmaApi() def exists(self): - # any platform associated must match - return any(platform['shortName'] == self.platform - for platform in self._gemma_api.platforms(self.dataset_short_name)) + return any( + (quantitation_type['id'] == self.quantitation_type or quantitation_type['name'] == self.quantitation_type + if self.quantitation_type else quantitation_type['isPreferred']) + and (quantitation_type['vectorType'] == self.vector_type.value if self.vector_type else True) + for quantitation_type in self._gemma_api.quantitation_types(self.dataset)) def __repr__(self): - return f'GemmaDatasetPlatform(dataset_short_name={self.dataset_short_name}, platform={self.platform})' + return f'GemmaDatasetQuantitationType(dataset={self.dataset}, quantitation_type={self.quantitation_type}, vector_type={self.vector_type})' class GemmaDatasetHasBatch(luigi.Target): """ diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index df16e5c..1391866 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -31,9 +31,8 @@ from .sources.local import DownloadLocalSample, DownloadLocalExperiment from .sources.sra import DownloadSraProject, DownloadSraExperiment from .sources.sra import ExtractSraProjectBatchInfo -from .targets import GemmaDatasetHasBatch -from .targets import GemmaDatasetPlatform -from .targets import RsemReference +from .targets import GemmaDatasetHasBatch, GemmaDatasetQuantitationType, GemmaDataVectorType, \ + RsemReference from .utils import RerunnableTaskMixin, no_retry from .utils import remove_task_output @@ -604,7 +603,9 @@ def subcommand_args(self): '-rpkm', fpkm.path] def output(self): - return GemmaDatasetPlatform(self.experiment_id, self.platform_short_name) + # there is also a log2cpm, but it is computed by Gemma + return [GemmaDatasetQuantitationType(self.experiment_id, 'Counts', vector_type=GemmaDataVectorType.RAW), + GemmaDatasetQuantitationType(self.experiment_id, 'RPKM', vector_type=GemmaDataVectorType.RAW)] class SubmitSingleCellExperimentDataToGemma(GemmaCliTask): subcommand = 'loadSingleCellData' @@ -642,7 +643,7 @@ def run(self): super().run() def output(self): - return GemmaDatasetPlatform(self.experiment_id, self.platform_short_name) + return GemmaDatasetQuantitationType(self.experiment_id, '10x MEX', vector_type=GemmaDataVectorType.SINGLE_CELL) class SubmitExperimentDataToGemma(GemmaTaskMixin, WrapperTask): def requires(self): diff --git a/tests/gemma-cli-mock b/tests/gemma-cli-mock index e69de29..fef66b5 100755 --- a/tests/gemma-cli-mock +++ b/tests/gemma-cli-mock @@ -0,0 +1 @@ +#!/usr/bin/env python \ No newline at end of file diff --git a/tests/test_targets.py b/tests/test_targets.py index 4015ab7..c85cd35 100644 --- a/tests/test_targets.py +++ b/tests/test_targets.py @@ -4,15 +4,23 @@ import pytest -from rnaseq_pipeline.targets import GemmaDatasetPlatform, GemmaDatasetHasBatch, ExpirableLocalTarget - -def test_gemma_targets(): - assert GemmaDatasetPlatform('GSE110256', 'Generic_mouse_ncbiIds').exists() +from rnaseq_pipeline.targets import GemmaDatasetHasBatch, GemmaDataVectorType, ExpirableLocalTarget, \ + GemmaDatasetQuantitationType @pytest.mark.skip('This test requires credentials.') def test_gemma_dataset_has_batch(): assert GemmaDatasetHasBatch('GSE110256').exists() +def test_gemma_dataset_quantitation_type(): + assert GemmaDatasetQuantitationType('GSE2018', vector_type=GemmaDataVectorType.RAW).exists() + assert GemmaDatasetQuantitationType('GSE2018', 'rma value').exists() + assert not GemmaDatasetQuantitationType('GSE2018', 'rma value 2').exists() + + assert GemmaDatasetQuantitationType('GSE2018', vector_type=GemmaDataVectorType.PROCESSED).exists() + assert GemmaDatasetQuantitationType('GSE2018', 'rma value - Processed version').exists() + + assert not GemmaDatasetQuantitationType('GSE2018', vector_type=GemmaDataVectorType.SINGLE_CELL).exists() + def test_expirable_local_target(): with tempfile.TemporaryDirectory() as tmp_dir: t = ExpirableLocalTarget(tmp_dir + '/test', ttl=timedelta(seconds=1)) From a3a7806f42e3f294fa27d71fb2b07dae25c5cafb Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 28 Oct 2025 07:56:44 -0700 Subject: [PATCH 36/45] Update cutadapt and MultiQC --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index d313628..99f3ec6 100644 --- a/environment.yml +++ b/environment.yml @@ -6,8 +6,8 @@ channels: dependencies: - python=3.12 - pip -- cutadapt==4.8 -- multiqc==1.29 +- cutadapt==4.9 +- multiqc==1.32 - polars-lts-cpu # for our older servers that lack support for AVX2 - sra-tools - fastqc==0.12.1 From d8fa72c0eba8ca0f4c88f58c526099d0e083ca86 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 28 Oct 2025 07:57:00 -0700 Subject: [PATCH 37/45] Remove redundant task definition and add keyword parameters --- rnaseq_pipeline/tasks.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 1391866..ae459e5 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -530,11 +530,6 @@ def run(self): reference_id=self.reference_id) for dst in download_sample_tasks] -class SubmitExperimentBatchInfoToGemma(RerunnableTaskMixin, GemmaCliTask): - """ - Submit the batch information of an experiment to Gemma. - """ - @requires(AlignSingleCellExperiment, TrimExperiment, QualityControlExperiment) class GenerateReportForSingleCellExperiment(RerunnableTaskMixin, luigi.Task): """Generate a report for single-cell""" @@ -691,13 +686,13 @@ class SubmitExperimentReportToGemma(RerunnableTaskMixin, GemmaCliTask): def requires(self): if self.assay_type == GemmaAssayType.BULK_RNA_SEQ: - return GenerateReportForExperiment(self.experiment_id, + return GenerateReportForExperiment(experiment_id=self.experiment_id, taxon=self.taxon, reference_id=self.reference_id, source='gemma', rerun=self.rerun) elif self.assay_type == GemmaAssayType.SINGLE_CELL_RNA_SEQ: - return GenerateReportForSingleCellExperiment(self.experiment_id, + return GenerateReportForSingleCellExperiment(experiment_id=self.experiment_id, reference_id=self.reference_id, source='gemma', rerun=self.rerun) From c9f29453001b8607375599f9f8fe67d7a5576dd3 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 28 Oct 2025 07:57:13 -0700 Subject: [PATCH 38/45] Migrate to pyproject.toml --- pyproject.toml | 28 ++++++++++++++++++++++++++++ setup.py | 25 ------------------------- 2 files changed, 28 insertions(+), 25 deletions(-) delete mode 100644 setup.py diff --git a/pyproject.toml b/pyproject.toml index 3d86a36..a597481 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,5 +2,33 @@ requires = ["setuptools"] build-backend = "setuptools.build_meta" +[project] +name = "rnaseq-pipeline" +version = "2.1.12" +description = "RNA-Seq pipeline for the Pavlidis Lab" +authors = [ + {name = "Guillaume Poirier-Morency", email = "poirigui@msl.ubc.ca"} +] +readme = "README.md" +license = "Unlicense" +license-files = ["LICENSE"] +requires-python = "==3.12.*" +dependencies = ['luigi', 'python-daemon<3.0.0', + 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@master', + 'requests', 'pandas'] + +[dependency-groups] +dev = [] +gsheet = ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'] +webviewer = ['Flask', 'gunicorn'] + +[project.scripts] +rnaseq-pipeline-cli = "rnaseq_pipeline.cli:main" +rnaseq-pipeline-cellranger = "rnaseq_pipeline.wrapped_tools:cellranger_wrapper" +rnaseq-pipeline-rsem-calculate-expression = "rnaseq_pipeline.wrapped_tools:rsem_calculate_expression_wrapper" + +[tool.setuptools] +packages = ["rnaseq_pipeline", "rnaseq_pipeline.sources", "rnaseq_pipeline.webviewer"] + [tool.mypy] plugins = ["luigi.mypy"] diff --git a/setup.py b/setup.py deleted file mode 100644 index f34e11a..0000000 --- a/setup.py +++ /dev/null @@ -1,25 +0,0 @@ -from setuptools import setup, find_packages - -setup(name='rnaseq_pipeline', - version='2.1.12', - description='RNA-Seq pipeline for the Pavlidis Lab', - license='Public Domain', - long_description='file: README.md', - long_description_content_type='text/markdown', - url='https://github.com/pavlidisLab/rnaseq-pipeline', - author='Guillaume Poirier-Morency', - author_email='poirigui@msl.ubc.ca', - classifiers=['License :: Public Domain'], - packages=find_packages(), - include_package_data=True, - install_requires=['luigi', 'python-daemon<3.0.0', - 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@feature-improved-sratools-support', - 'requests', 'pandas'], - extras_require={ - 'gsheet': ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'], - 'webviewer': ['Flask', 'gunicorn']}, - entry_points={'console_scripts': [ - 'rnaseq-pipeline-cli = rnaseq_pipeline.cli:main', - 'rnaseq-pipeline-cellranger = rnaseq_pipeline.wrapped_tools:cellranger_wrapper', - 'rnaseq-pipeline-rsem-calculate-expression = rnaseq_pipeline.wrapped_tools:rsem_calculate_expression_wrapper' - ]}) From dd711b6e4e5fc9fab4ff312aa4a4ce3f6c03b7d0 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Wed, 29 Oct 2025 20:42:43 -0700 Subject: [PATCH 39/45] Move gsheet and webviewer in optional dependencies --- pyproject.toml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a597481..f5cc511 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,11 +17,13 @@ dependencies = ['luigi', 'python-daemon<3.0.0', 'bioluigi@git+https://github.com/PavlidisLab/bioluigi@master', 'requests', 'pandas'] -[dependency-groups] -dev = [] +[project.optional-dependencies] gsheet = ['google-api-python-client', 'google-auth-httplib2', 'google-auth-oauthlib', 'pyxdg'] webviewer = ['Flask', 'gunicorn'] +[dependency-groups] +dev = ["pytest", "mypy"] + [project.scripts] rnaseq-pipeline-cli = "rnaseq_pipeline.cli:main" rnaseq-pipeline-cellranger = "rnaseq_pipeline.wrapped_tools:cellranger_wrapper" From 6ba8539055741c4fa12e8085de49e0ed011bb17b Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 04:36:10 -0700 Subject: [PATCH 40/45] Remove unused IlluminaFastqHeader and CheckAfterCompleteMixin --- rnaseq_pipeline/utils.py | 39 --------------------------------------- 1 file changed, 39 deletions(-) diff --git a/rnaseq_pipeline/utils.py b/rnaseq_pipeline/utils.py index 469ca7b..970377d 100644 --- a/rnaseq_pipeline/utils.py +++ b/rnaseq_pipeline/utils.py @@ -5,36 +5,6 @@ logger = logging.getLogger(__name__) -class IlluminaFastqHeader: - @classmethod - def parse(cls, s): - pieces = s.split(':') - if len(pieces) == 5: - device, flowcell_lane, tile, x, y = pieces - return cls(device, flowcell_lane=flowcell_lane, tile=tile, x=x, y=y) - elif len(pieces) == 7: - return cls(*pieces) - else: - raise TypeError('Unsupported Illumina FASTQ header format {}.'.format(s)) - - def __init__(self, device, run=None, flowcell=None, flowcell_lane=None, tile=None, x=None, y=None): - self.device = device - self.run = run - self.flowcell = flowcell - self.flowcell_lane = flowcell_lane - self.tile = tile - self.x = x - self.y = y - - @property - def batch_factor(self): - if self.flowcell is None: - return self.device, self.flowcell_lane - return self.device, self.flowcell, self.flowcell_lane - -def parse_illumina_fastq_header(s): - return IlluminaFastqHeader(*s.split(':')) - def max_retry(count): """ Set the maximum number of time a task can be retried before being disabled @@ -68,15 +38,6 @@ def run(self): def complete(self): return (not self.rerun or self._has_rerun) and super().complete() -class CheckAfterCompleteMixin(luigi.Task): - """Ensures that a task is completed after a successful run().""" - - def run(self): - ret = super().run() - if not self.complete(): - raise RuntimeError('{} is not completed after successful run().'.format(repr(self))) - return ret - def remove_task_output(task): logger.info('Cleaning up %s...', repr(task)) for out in flatten_output(task): From 2e9afeee0b45db200f522e3186e01d6060b7216d Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 04:59:11 -0700 Subject: [PATCH 41/45] Add a chemistry option to AlignSingleCellSample --- rnaseq_pipeline/tasks.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index ae459e5..551557c 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -490,6 +490,8 @@ class AlignSingleCellSample(DynamicWrapperTask): experiment_id: str sample_id: str + chemistry: Optional[str] = luigi.OptionalParameter(default=None, positional=False) + def run(self): fastqs_dir, transcriptome_dir = self.input() yield CellRangerCount( @@ -497,6 +499,7 @@ def run(self): transcriptome_dir=transcriptome_dir, fastqs_dir=fastqs_dir, output_dir=self.output().path, + chemistry=self.chemistry, # TODO: add an avx feature on slurm scheduler_extra_args=['--constraint', 'thrd64', '--gres=scratch=300G'], walltime=datetime.timedelta(days=1) @@ -518,6 +521,7 @@ class AlignSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): source: str = luigi.ChoiceParameter(default='local', choices=['gemma', 'geo', 'sra', 'arrayexpress', 'local'], positional=False) reference_id: str = luigi.Parameter(positional=False) + chemistry: Optional[str] = luigi.OptionalParameter(default=None, positional=False) def requires(self): return DownloadExperiment(self.experiment_id, source=self.source).requires().requires() @@ -527,7 +531,8 @@ def run(self): yield [AlignSingleCellSample(experiment_id=self.experiment_id, sample_id=dst.sample_id, source=self.source, - reference_id=self.reference_id) + reference_id=self.reference_id, + chemistry=self.chemistry) for dst in download_sample_tasks] @requires(AlignSingleCellExperiment, TrimExperiment, QualityControlExperiment) From 916e16851414e4822f0bf01229d8c28fe7ec8078 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 05:00:17 -0700 Subject: [PATCH 42/45] Fix types and imports in tasks.py --- rnaseq_pipeline/tasks.py | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 551557c..6d86253 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -6,21 +6,22 @@ import uuid from glob import glob, iglob from os import unlink, makedirs, link, symlink -from os.path import dirname, join, basename, splitext +from os.path import dirname, join, basename +from typing import Optional import luigi import luigi.task import pandas as pd import requests -from luigi import WrapperTask -from luigi.task import flatten, flatten_output -from luigi.util import requires - from bioluigi.scheduled_external_program import ScheduledExternalProgramTask from bioluigi.tasks import fastqc, multiqc from bioluigi.tasks.cellranger import CellRangerCount from bioluigi.tasks.utils import DynamicTaskWithOutputMixin, DynamicWrapperTask from bioluigi.tasks.utils import TaskWithOutputMixin +from luigi import WrapperTask +from luigi.task import flatten, flatten_output +from luigi.util import requires + from rnaseq_pipeline.config import Config from .gemma import GemmaAssayType, GemmaTaskMixin, GemmaConfig from .gemma import GemmaCliTask @@ -86,15 +87,15 @@ class DownloadExperiment(TaskWithOutputMixin, luigi.WrapperTask): def requires(self): if self.source == 'gemma': - return DownloadGemmaExperiment(self.experiment_id) + return DownloadGemmaExperiment(experiment_id=self.experiment_id) elif self.source == 'geo': - return DownloadGeoSeries(self.experiment_id) + return DownloadGeoSeries(experiment_id=self.experiment_id) elif self.source == 'sra': - return DownloadSraProject(self.experiment_id) + return DownloadSraProject(experiment_id=self.experiment_id) elif self.source == 'arrayexpress': - return DownloadArrayExpressExperiment(self.experiment_id) + return DownloadArrayExpressExperiment(experiment_id=self.experiment_id) elif self.source == 'local': - return DownloadLocalExperiment(self.experiment_id) + return DownloadLocalExperiment(experiment_id=self.experiment_id) else: raise ValueError('Unknown download source for experiment: {}.') @@ -202,7 +203,7 @@ def _get_destdir(self, fastq_in: luigi.LocalTarget): # TODO: make the run_id part of the output of TrimSample run_id = basename(dirname(fastq_in.path)) # fastqc output is a directory, so to make this atomic, we need a sub-directory for each file being QCed - filename = basename(fastq_in.path).removesuffix('.fastq.gz') + filename = str(basename(fastq_in.path).removesuffix('.fastq.gz')) return join(cfg.OUTPUT_DIR, cfg.DATAQCDIR, self.experiment_id, self.sample_id, run_id, filename) class QualityControlExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): @@ -405,7 +406,7 @@ def run(self): with open(sample_names_file, 'w') as out: for sample_trim_dirs in trim_sample_dirs: for lane_trim in sample_trim_dirs: - run_id = '___'.join(basename(lt.path).removesuffix('.fastq.gz') + run_id = '___'.join(str(basename(lt.path).removesuffix('.fastq.gz')) for lt in lane_trim) sample_id = basename(dirname(dirname(lane_trim[0].path))) out.write(f'{run_id}\t{sample_id}_{run_id}\n') @@ -511,6 +512,7 @@ def output(self): @requires(DownloadExperiment) class OrganizeSingleCellExperiment(DynamicTaskWithOutputMixin, DynamicWrapperTask): + experiment_id: str def run(self): download_sample_tasks = next(self.requires().run()) yield [OrganizeSingleCellSample(experiment_id=self.experiment_id, sample_id=task.sample_id) @@ -555,7 +557,7 @@ def run(self): with open(sample_names_file, 'w') as out: for sample_trim_dirs in trim_sample_dirs: for lane_trim in sample_trim_dirs: - run_id = '___'.join(basename(lt.path).removesuffix('.fastq.gz') + run_id = '___'.join(str(basename(lt.path).removesuffix('.fastq.gz')) for lt in lane_trim) sample_id = basename(dirname(dirname(lane_trim[0].path))) out.write(f'{run_id}\t{sample_id}_{run_id}\n') From 251b7b64c9b41c276ad48d0548bac674d2db2b55 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 05:36:22 -0700 Subject: [PATCH 43/45] fixup! Remove unused IlluminaFastqHeader and CheckAfterCompleteMixin --- tests/test_utils.py | 26 -------------------------- 1 file changed, 26 deletions(-) delete mode 100644 tests/test_utils.py diff --git a/tests/test_utils.py b/tests/test_utils.py deleted file mode 100644 index 165da86..0000000 --- a/tests/test_utils.py +++ /dev/null @@ -1,26 +0,0 @@ -from rnaseq_pipeline.utils import * - -def test_parse_illumina_fastq_header(): - # 1.4 flavour - fastq_header = IlluminaFastqHeader.parse('HS32_14737:1:2104:16434:41647') - assert fastq_header.flowcell_lane == '1' - assert fastq_header.batch_factor == ('HS32_14737', '1') - - # make sure that we can combine it with a GEO platform id - assert ('GPL1111',) + fastq_header.batch_factor == ('GPL1111', 'HS32_14737', '1') - - # 1.8 flavour - fastq_header = IlluminaFastqHeader.parse('NIRVANA:127:C08GPACXX:4:1101:1487:2137') - assert fastq_header.device == 'NIRVANA' - assert fastq_header.batch_factor == ('NIRVANA', 'C08GPACXX', '4') - - # make sure that we can combine it with a GEO platform id - assert ('GPL1111',) + fastq_header.batch_factor == ('GPL1111', 'NIRVANA', 'C08GPACXX', '4') - - IlluminaFastqHeader.parse('HS19_09559:4:1101:1591:13817') - -def test_parse_sra_fastq_header(): - _, fastq_header, _ = '@SRR8267714.1.2 HS19_09559:4:1101:1571:31744 length=100'.split() - fastq_header = IlluminaFastqHeader.parse(fastq_header) - assert fastq_header.device == 'HS19_09559' - assert fastq_header.flowcell_lane == '4' From d5e46ae54e824ce39217bdd420372840bc378f15 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 05:51:13 -0700 Subject: [PATCH 44/45] Fix incorrect logger usage in sra.py --- rnaseq_pipeline/sources/sra.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index f0528f2..d010210 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -240,7 +240,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: read_types = fastq_load_read_types elif sra_fastq_files: - logging.warning( + logger.warning( "%s: The SRA files: %s do not match arguments passed to fastq-load.py: %s. The filenames passed to fastq-load.py will be used instead: %s.", srr, ', '.join(sf.attrib['filename'] for sf in sra_fastq_files), @@ -256,7 +256,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: issues |= SraRunIssue.MISMATCHED_FASTQ_LOAD_OPTIONS else: - logging.warning( + logger.warning( "%s: No SRA files found, but the arguments of fastq-load.py are present: %s. The filenames passed to fastq-load.py will be used: %s.", srr, ' '.join(k + '=' + v if v else 'k' for k, v in options.items()), ', '.join(fastq_load_files)) fastq_filenames = fastq_load_files @@ -269,7 +269,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: # check for 10x BAM files elif sra_10x_bam_files: - logging.info('%s: Using 10x Genomics BAM files do determine read layout.', srr) + logger.info('%s: Using 10x Genomics BAM files do determine read layout.', srr) # we have to read the file(s), unfortunately if len(sra_10x_bam_files) > 1: @@ -293,7 +293,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: 'Mixture of sequencing layouts in a single 10x BAM file are not supported.') if flowcells: - logging.info('%s: Detected read types from BAM file %s: %s', srr, bam_file.attrib['filename'], + logger.info('%s: Detected read types from BAM file %s: %s', srr, bam_file.attrib['filename'], ', '.join(rt.name for rt in bam_read_types)) # FIXME: report FASTQ filenames for all flowcells and lanes flowcell = next(iter(flowcells.values())) @@ -312,7 +312,7 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: bam_file_urls = [bam_file.attrib['url']] bam_fastq_filenames = get_fastq_filenames_for_10x_sequencing_layout(flowcells) else: - logging.warning('%s: Failed to detect read types from BAM file, ignoring that run.', srr) + logger.warning('%s: Failed to detect read types from BAM file, ignoring that run.', srr) issues |= SraRunIssue.INVALID_RUN if include_invalid_runs: result.append(SraRunMetadata(srx, srr, @@ -459,9 +459,9 @@ def read_bam_header(srr, filename, url): """Read and cache the header of a SRA BAM file.""" bam_header_file = join(cfg.OUTPUT_DIR, sra_config.bam_headers_cache_dir, srr + '.bam-header.txt') if os.path.exists(bam_header_file): - logging.info('%s: Using cached 10x BAM header from %s...', srr, bam_header_file) + logger.info('%s: Using cached 10x BAM header from %s...', srr, bam_header_file) else: - logging.info('%s: Reading header from 10x BAM file %s from %s to %s...', srr, + logger.info('%s: Reading header from 10x BAM file %s from %s to %s...', srr, filename, url, bam_header_file) os.makedirs(os.path.dirname(bam_header_file), exist_ok=True) with open(bam_header_file, 'w') as f: From dcadc15c1cb094f223ae8564d219f19e88ef0021 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Thu, 30 Oct 2025 05:54:51 -0700 Subject: [PATCH 45/45] Downgrade warning for no fastq-load.py options to info --- rnaseq_pipeline/sources/sra.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py index d010210..9daca98 100644 --- a/rnaseq_pipeline/sources/sra.py +++ b/rnaseq_pipeline/sources/sra.py @@ -180,7 +180,8 @@ def read_xml_metadata(path, include_invalid_runs=False) -> List[SraRunMetadata]: if o in options: fastq_load_files.append(options[o]) else: - logger.warning('%s: The fastq-load.py loader does not have any option.', srr) + # this is excessively common, so does not warrant a warning + logger.info('%s: The fastq-load.py loader does not have any option.', srr) fastq_load_files = None issues |= SraRunIssue.NO_FASTQ_LOAD_OPTIONS else: