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The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (CUT&RUN)

GSE281499 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 50 samples Submitted 2025/07/09 Platform GPL24247Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 50 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
50 samples: 22 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
The transcription factor BATF pioneers the differentiation program of effector CD8(+) T cells through the interaction with IRF4Cell reports · 2025
Summary (written by the submitters)
The transcription factor BATF plays critical roles in the differentiation of various immune cells, including CD8+ T cells. Here, we demonstrated that BATF controls epigenomic and transcriptomic reprogramming of CD8+ T cells at an early phase of acute viral infection, thereby promoting the differentiation of cytolytic effector CD8+ T cells.
Read the full summary ↓
Loss of BATF drastically perturbed gene expression, chromatin accessibility, and the bindings of key transcription factors including Jun, T-bet, and IRF4. The direct interaction with IRF4 was essential for BATF-mediated effector differentiation, as the BATF mutant lacking this interaction failed to induce proper chromatin remodeling and proliferation of antigen-specific CD8+ T cells. Notably, IRF4 binding was exhaustively dependent on BATF, whereas BATF retained binding capacity even in IRF4-deficient CD8+ T cells. Furthermore, BATF initiated chromatin remodeling in the absence of IRF4, whereas subsequent dynamic epigenomic reorganization required IRF4. Our data proposed that BATF serves as a “pioneer transcription factor” spearheading the reorganization of chromatin architecture upon antigen encounter, followed by further rearrangement of epigenomic and transcriptomic landscapes through the cooperation with IRF4.
Published in
The transcription factor BATF pioneers the differentiation program of effector CD8(+) T cells through the interaction with IRF4
Fujisawa S, Tanabe Y, Hojo A et al. · Cell reports 2025 · PMID 40773348 · doi:10.1016/j.celrep.2025.116129
This dataset
Open GSE281499 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 GSE281499_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 PRJNA1184149 and SRA study SRP544227. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40773348) ↗
Study design
22 conditions, mostly in duplicate
WT_nIgG ×3 WT_BATF ×2 WT_IRF4 ×2 BatfKO_IRF4 ×2 WT_Tbet ×2 BatfKO_Tbet ×2 WT_JunB ×2 BatfKO_JunB ×2 +19 more

Supports a between-group comparison across 45 samples.

How we read this: 22 replicated groups read from 50 sample titles; they account for 45 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

+ 10 more — browse all 50 samples with per-sample file links →

Datasets on a similar topic

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