scCRISPR screens of CD8⁺ T cells in young vs. aged tumors and tdLNs
Single-cell RNA-seq · mouse · 11 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 4 × scPerturb_Young vs 4 × scPerturb_Aged vs 2 × scPerturb_YoungtdLNGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE306058_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1309035 and SRA study SRP610455. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 3 replicated groups read from 11 sample titles; they account for 10 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9192232 scPerturb_Young1 scPerturb_Young
- GSM9192233 scPerturb_Young2 scPerturb_Young
- GSM9192234 scPerturb_Young3 scPerturb_Young
- GSM9192235 scPerturb_Young4 scPerturb_Young
- GSM9192236 scPerturb_Aged1 scPerturb_Aged
- GSM9192237 scPerturb_Aged2 scPerturb_Aged
- GSM9192238 scPerturb_Aged3 scPerturb_Aged
- GSM9192239 scPerturb_Aged4 scPerturb_Aged
- GSM9192240 scPerturb_YoungtdLN1 scPerturb_YoungtdLN
- GSM9192241 scPerturb_YoungtdLN2 scPerturb_YoungtdLN
- GSM9192242 scPerturb_AgedtdLN1
- GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares cd8, screens
- GSE266454 AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK 21 samples shares cd8, aged
- GSE334890 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors 48 samples shares cd8, screens
- GSE282210 Transcriptome analysis of quiescent livers and regenerating livers after partial hepatectomy (PH) in young and aged mice 133 samples shares young, aged
- GSE270016 Rejuvenation of aged oocyte through exposure to young follicular microenvironment 45 samples shares young, aged
- GSE283201 Comparative gene expression profiling analysis of hippocampus and liver RNA-seq data for young (3-month-old) and aged (22-month-old) WT mice in both control and ethanol feeding conditions. 32 samples shares young, aged
- GSE303183 The skeletal muscle of aged male mice exhibits a sustained growth regulatory transcriptional profile following prolonged glucocorticoid exposure compared to young males 24 samples shares young, aged
- GSE316541 α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment [CD8+T] 27 samples shares cd8
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.