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Smad4 and Eomes converge on a shared transcriptional program associated with inflammatory CD8 T-cell differentiation

GSE338265 Mus musculus (mouse) RNA-seq (gene expression) 31 samples Submitted 2026/07/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 31 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
31 samples: 11 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
The ability of CD8 T cells to mediate protective immunity while limiting immunopathology depends on critical transcription factors such as Smad4 and Eomes that regulate differentiation of activated CTLs. Disruption of transcriptional programs mediated by Eomes (30-32) and Smad4 (26, 33, 34) in activated CTLs has been implicated in viral infections, chronic inflammation and cancer.
Read the full summary ↓
Smad4 and Eomes have been shown to be critical for differentiation of memory cells, particularly TRM cells. To understand the gene regulation programs mediated by Smad4 and Eomes, we have done an integrated RNAseq and ChIPseq analysis using CD8 T cells that are isolated from Smad4KO (S4KO), EomesKO, and Smad3/Smad4-DKO (S34-DKO) mice. We identified overlapping and distinct gene expression programs associated with Smad4 and Eomes that shape activated CD8 T cell identity and functional bias. They act as critical regulators of genes involved in T cell differentiation, metabolic programming and epigenetic control in CD8 T cells. Smad4 and Eomes regulate the genes involved in tissue residency and OXPHOS-linked mitochondrial bioenergetics. Finally, we showed that canonical TGF signaling is active in the absence of Smad4 or Eomes and abrogated only when both Smad3 and Smad4 are deleted. Surprisingly, CD8 T cells lacking both Smad3 and Smad4 are more enriched for TRM signature genes compared to Smad4 or Eomes-deficient CD8 T cells.
This dataset
Open GSE338265 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 GSE338265_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 PRJNA1493078 and SRA study SRP716992. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in triplicate
S34KO_12hr_NoTGF ×4 S34KO_12hr_TGF ×4 WT_0h ×3 WT_12hr_NoTGF ×3 WT_12hr_TGF ×3 S4KO_12hr_NoTGF ×3 S4KO_12hr_TGF ×3 EomesKO_0h ×2 +3 more

Supports a between-group comparison across 31 samples.

How we read this: 11 replicated groups read from 31 sample titles; they account for 31 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
Datasets on a similar topic

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