GEO series

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

GSE322657 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2026/03/10 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 10 samples: 4 × CnT_D8_aKLF2 vs 2 × CnT_D8_aIgG vs 2 × CnT_n_aKLF2 vs 2 × CnT_n_aIgGGroups 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 GSE322657 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE322657_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1430833 and SRA study SRP680340. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41871244) ↗

Study design

4 × CnT_D8_aKLF2 vs 2 × CnT_D8_aIgG vs 2 × CnT_n_aKLF2 vs 2 × CnT_n_aIgG

Supports a between-group comparison across 10 samples.

How we read this: 4 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

GSM9556273 CnT_D8_aKLF2_rep1 CnT_D8_aKLF2
GSM9556274 CnT_D8_aKLF2_rep2 CnT_D8_aKLF2
GSM9556275 CnT_D8_aKLF2_rep3 CnT_D8_aKLF2
GSM9556276 CnT_D8_aKLF2_rep4 CnT_D8_aKLF2
GSM9556277 CnT_D8_aIgG_rep1 CnT_D8_aIgG
GSM9556278 CnT_D8_aIgG_rep2 CnT_D8_aIgG
GSM9556279 CnT_n_aKLF2_rep1 CnT_n_aKLF2
GSM9556280 CnT_n_aKLF2_rep2 CnT_n_aKLF2
GSM9556281 CnT_n_aIgG_rep1 CnT_n_aIgG
GSM9556282 CnT_n_aIgG_rep2 CnT_n_aIgG

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