GEO series

Basal level of ATF4 promotes T cell readiness for activation-induced proliferation [RNA-seq]

GSE288143 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2026/01/21 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 samples: 6 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.
Paper: Basal level of ATF4 promotes T cell readiness for activation-induced proliferationiScience · 2026

Summary (written by the submitters)

Stress responding elements such as eIF2α phosphorylation are either upregulated or required during late-phase T cell activation and differentiation. However, it is not well understood whether these elements are essential within the first 12-24 hours post-stimulation, a period when mitochondrial activation and metabolic reprogramming are critical.

Read the full summary ↓

Here, we demonstrate that T cell activation-induced mTOR and GCN2 phosphorylation leads to the upregulation of ATF4 protein as early as 12 hours after stimulation. This early induction of ATF4 has transcriptional activities that positively or negatively regulate stress response, signaling, and metabolism. Loss of Atf4 in T cells alters transcriptome dynamics, impairs amino acid transport and biosynthesis, and disrupts cellular adaptive responses to ER stress and oxidative stress. It also hinders cell growth, resulting in defective effector cell differentiation in vitro or in vivo in a chronic LCMV infection model. Our findings suggest that a basal level of ATF4 during the early phase of T cell activation enhances the preparedness of cells to cope with integrated nutritional, protein folding, and oxidative stresses during the activation course. This, in turn, protects cells from stress-related cell death or senescence.

Published in

Basal level of ATF4 promotes T cell readiness for activation-induced proliferation

Yi Y, Luo C, Wang J et al. · iScience 2026 · PMID 41550765 · doi:10.1016/j.isci.2025.114277

This dataset

Open GSE288143 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 GSE288143_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 PRJNA1216275 and SRA study SRP560230. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41550765) ↗

Study design

6 conditions, mostly in duplicate

Mus CD8+ T cell, WT, 12h , ×2 Mus CD8+ T cell, KO, 12h , ×2 Mus CD8+ T cell, WT, 24h , ×2 Mus CD8+ T cell, KO, 24h , ×2 Mus CD8+ T cell, WT, 48h , ×2 Mus CD8+ T cell, KO, 48h , ×2 Mus CD8+ T cell, WT, 0h ×1 Mus CD8+ T cell, KO, 0h ×1

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 12 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

GSM8759839 Mus CD8+ T cell, WT, 0h
GSM8759840 Mus CD8+ T cell, KO, 0h
GSM8759841 Mus CD8+ T cell, WT, 12h , rep1 Mus CD8+ T cell, WT, 12…
GSM8759842 Mus CD8+ T cell, WT, 12h , rep2 Mus CD8+ T cell, WT, 12…
GSM8759843 Mus CD8+ T cell, KO, 12h , rep1 Mus CD8+ T cell, KO, 12…
GSM8759844 Mus CD8+ T cell, KO, 12h , rep2 Mus CD8+ T cell, KO, 12…
GSM8759845 Mus CD8+ T cell, WT, 24h , rep1 Mus CD8+ T cell, WT, 24…
GSM8759846 Mus CD8+ T cell, WT, 24h , rep2 Mus CD8+ T cell, WT, 24…
GSM8759847 Mus CD8+ T cell, KO, 24h , rep1 Mus CD8+ T cell, KO, 24…
GSM8759848 Mus CD8+ T cell, KO, 24h , rep2 Mus CD8+ T cell, KO, 24…
GSM8759849 Mus CD8+ T cell, WT, 48h , rep1 Mus CD8+ T cell, WT, 48…
GSM8759850 Mus CD8+ T cell, WT, 48h , rep2 Mus CD8+ T cell, WT, 48…
GSM8759851 Mus CD8+ T cell, KO, 48h , rep1 Mus CD8+ T cell, KO, 48…
GSM8759852 Mus CD8+ T cell, KO, 48h , rep2 Mus CD8+ T cell, KO, 48…

Datasets on a similar topic

GSE305975 Basal level of ATF4 promotes T cell readiness for activation-induced proliferation 29 samples shares atf4, activation-induced, proliferation, readiness, promotes, basal, level
GSE305890 Basal level of ATF4 promotes T cell readiness for activation-induced proliferation [CUT&Run] 11 samples shares atf4, activation-induced, proliferation, readiness, promotes, basal, level
GSE281443 Pre-occupied ATF4 relies on CEBPγ co-binding for robust transcription activation during integrated stress response [RNA-seq] 19 samples shares atf4, rna-seq
GSE287894 Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stress [Atf4 & Cebpg KO RNA-seq] 18 samples shares atf4, rna-seq
GSE303803 Pre-occupied ATF4 relies on CEBPγ co-binding for robust transcription activation during integrated stress response [C2C12_Thap_RNA-seq] 12 samples shares atf4, rna-seq
GSE235798 Atf4 promotes erythroid differentiation by regulating ribosome biogenesis via RPS19BP1 6 samples shares atf4, promotes
GSE285141 Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [RNA-seq] 81 samples shares proliferation, rna-seq
GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares proliferation, promotes

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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.