GEO series

SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [RNA-seq]

GSE275974 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/07/16 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 10 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: 10 samples: 5 × sgSatb vs 5 × sgCtrlGroups 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.
Paper: SATB1 is a key regulator of quiescence in stem-like CD8(+) T cellsNature immunology · 2025

Summary (written by the submitters)

Chronic infections and cancers induce CD8+ T cell exhaustion, but within this exhausted CD8+ T cell pool, a self-renewing, stem-like subset known as progenitor CD8+ T (TPRO) cells play a crucial role in maintaining long-term immunity. These TPRO cells exhibit stem-like characteristics, including quiescence, multipotency, and self-renewal, which are the cardinal features of memory T cells.

Read the full summary ↓

However, the mechanisms that preserve their stem-like properties under chronic antigen stimulation remain unclear. In this study, we identified that SATB1 as a shared feature is highly expressed in both TPRO and memory CD8+ T cells. While the role of SATB1 in stem-like CD8+ T cells remains unknown, its function as epigenetic regulator in promoting quiescence in hematopoietic stem cells led us to hypothesize that SATB1 plays a pivotal role in regulating the stemness of TPRO and memory CD8+ T cells. To test this hypothesis, we employed CRISPR-mediated gene editing to delete Satb1 gene specifically in CD8+ T cells. Upon chronic LCMV infection, we found that SATB1-deficient CD8+ T cells failed to maintain TPRO subset with enhanced transition towards terminally differentiated cells. Similarly, the SATB1 deficiency in acute viral infection impaired the formation of memory CD8+ T cells. Mechanistically, our multi-omic assays revealed that SATB1 regulates the chromatin accessibility and transcriptional activities of stemness-associated genes, such asTcf7, Bach2,andMyb. Overall, our results underscore the critical role of SATB1 in maintaining the transcriptional and epigenetic features of stem-like CD8+ T cells, shedding light on the previously unappreciated regulatory mechanisms that sustain the stemness of antigen-specific CD8+ T cells.

Published in

SATB1 is a key regulator of quiescence in stem-like CD8(+) T cells

Lin S, Niu H, Zhang Y et al. · Nature immunology 2025 · PMID 40847243 · doi:10.1038/s41590-025-02257-w

This dataset

Open GSE275974 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE275974_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1154003 and SRA study SRP529416. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40847243) ↗

Study design

5 × sgSatb vs 5 × sgCtrl

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 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.

Samples in this study

GSM8488879 sgSatb_rep1 sgSatb
GSM8488880 sgSatb_rep2 sgSatb
GSM8488881 sgSatb_rep3 sgSatb
GSM8488882 sgSatb_rep4 sgSatb
GSM8488883 sgSatb_rep5 sgSatb
GSM8488884 sgCtrl_rep1 sgCtrl
GSM8488885 sgCtrl_rep2 sgCtrl
GSM8488886 sgCtrl_rep3 sgCtrl
GSM8488887 sgCtrl_rep4 sgCtrl
GSM8488888 sgCtrl_rep5 sgCtrl

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