NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment (RNA-Seq)
RNA-seq (gene expression) · mouse · 18 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 18 samples: 8 conditions, mostly in duplicateGroups 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.
Read the full summary ↓
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 GSE266287_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1106511 and SRA study SRP504941. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 8 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8244438 Nr4a1RFP+ TIL-1 Nr4a1RFP+ TIL
- GSM8244439 Nr4a1RFP+ TIL-2 Nr4a1RFP+ TIL
- GSM8244440 Tim-3+ TIL-1 Tim-3+ TIL
- GSM8244441 Tim-3+ TIL-2 Tim-3+ TIL
- GSM8244442 Nr4a1-OV-1 Nr4a1-OV
- GSM8244443 Nr4a1-OV-2 Nr4a1-OV
- GSM8244444 RV-GFP-1 RV-GFP
- GSM8244445 RV-GFP-2 RV-GFP
- GSM8244446 Nr4a1 WT-1 Nr4a1 WT
- GSM8244447 Nr4a1 WT-2 Nr4a1 WT
- GSM8244448 Nr4a1 KO-1 Nr4a1 KO
- GSM8244449 Nr4a1 KO-2 Nr4a1 KO
- GSM8244450 Ly108+ Nr4a1 WT TIL-1 Ly108+ Nr4a1 WT TIL
- GSM8244451 Ly108+ Nr4a1 WT TIL-2 Ly108+ Nr4a1 WT TIL
- GSM8244452 Ly108+ Nr4a1 WT TIL-3 Ly108+ Nr4a1 WT TIL
- GSM8244453 Ly108+ Nr4a1 KO TIL-1 Ly108+ Nr4a1 KO TIL
- GSM8244454 Ly108+ Nr4a1 KO TIL-2 Ly108+ Nr4a1 KO TIL
- GSM8244455 Ly108+ Nr4a1 KO TIL-3 Ly108+ Nr4a1 KO TIL
- GSE275974 SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [RNA-seq] 10 samples shares cd8, stem-like, rna-seq
- 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, rna-seq
- GSE316541 α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment [CD8+T] 27 samples shares cd8, microenvironment
- GSE290839 PD-1 regulates tumor-infiltrating CD8+ T cells in both a cell-intrinsic and cell-extrinsic fashion [scRNA-seq] 20 samples shares cd8, rna-seq
- GSE269347 Daunorubicin-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ prolifeating T cells [scRNA-Seq] 16 samples shares cd8, rna-seq
- GSE215759 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq] 15 samples shares cd8, rna-seq
- GSE316540 α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment 9 samples shares cd8, microenvironment
- GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares cd8, rna-seq
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.