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KLF2 overrides the resident memory CD8 T cell differentiation program, in opposition to KLF3

GSE324376 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2026/03/10 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 6 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.
Paper
KLF2 overrides the resident memory CD8 T cell differentiation program, in opposition to KLF3Proceedings of the National Academy of Sciences of the United States of America · 2026
Summary (written by the submitters)
Numerous transcriptional regulators have been associated with the differentiation pathways that lead to recirculating versus tissue-resident memory T cells. However, it is unclear whether independent, coordinated expression of these regulators is required to determine residency versus recirculation, or whether there is a hierarchy, with some factors playing a dominant role in controlling T cell trafficking.
Read the full summary ↓
We report that ablation of the gene encoding Kruppel-like factor 2 (KLF2) during CD8+ T cell activation leads to rapid transcriptional reprograming, such that effector T cells fail to recirculate and prematurely acquire canonical phenotypic and transcriptional characteristics of resident memory cells (TRM). Klf2-deficient memory CD8+ T cells retained the capacity to undergo recall responses, including in vivo pathogen control. These data suggest KLF2 diverts CD8+ T cells from the TRM differentiation program. In contrast, ablation of another member of the KLF family, KLF3, enhanced differentiation of some recirculating T cell subsets and limited production of TRM in lymphoid tissues. However, both KLF2 and KLF3 were required for differentiation of long-lived effector cells, suggesting cooperation between these factors in some situations. These findings indicate KLFs occupy a central nexus in coordinating activated CD8+ T cell differentiation and trafficking.
Published in
KLF2 overrides the resident memory CD8 T cell differentiation program, in opposition to KLF3
DePauw TA, Gai K, Shen J et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 41871244 · doi:10.1073/pnas.2533700123
This dataset
Open GSE324376 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 GSE324376_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 PRJNA1434513 and SRA study SRP682375. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41871244) ↗
Study design
6 conditions, mostly in triplicate
spleen CD8+ T cells, KLF2 KO, D7, ×4 spleen CD8+ T cells, KLF2 control, D7, ×4 spleen CD8+ T cells, KLF2 KO, D25, ×3 spleen CD8+ T cells, KLF3 KO, D25, ×3 spleen CD8+ T cells, KLF2 control, D25, ×3 spleen CD8+ T cells, KLF3 control, D25, ×3

Supports a between-group comparison across 20 samples.

How we read this: 6 replicated groups read from 20 sample titles; they account for 20 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
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