GEO series

Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [ATAC_bulk_adult]

GSE297597 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2025/08/28 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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: 14 samples: 4 × D3 TIR1 vs 4 × D3 WT vs 3 × D7 TIR1 vs 3 × D7 WTGroups 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: Temporal and context-dependent requirements for the transcription factor Foxp3 expression in regulatory T cellsNature immunology · 2025

Summary (written by the submitters)

Regulatory T (Treg) cells, characterized by expression of the lineage-defining transcription factor Foxp3, are critical gatekeepers of immune homeostasis. While Foxp3’s essential role in Treg cell development is well established, the precise mechanisms by which Foxp3 governs the Treg-specific transcriptional network remain incompletely understood.

Read the full summary ↓

Here, we employed a novel chemogenetic model that enables inducible, time-controlled degradation of Foxp3 protein in vivo to dissect its stage-specific functions. We show that Foxp3 is indispensable for the establishment of the Treg transcriptional program and the acquisition of suppressive function during thymic differentiation and in newly generated peripheral Treg cells. In contrast, degradation of Foxp3 in fully differentiated, mature Treg cells resulted in surprisingly minimal transcriptional changes and largely preserved suppressive capacity, affecting only a small subset of genes highly enriched for direct Foxp3 targets. Strikingly, intratumoral Treg cells were uniquely sensitive to Foxp3 loss, leading to impaired suppressive function and enhanced tumor rejection. These findings uncover a differential, context-dependent requirement for Foxp3 across Treg cell ontogeny, highlighting a distinct, largely indirect mechanism by which Foxp3 establishes — and to a more limited extent maintains — Treg identity and function.

Published in

Temporal and context-dependent requirements for the transcription factor Foxp3 expression in regulatory T cells

Hu W, Dolsten GA, Wang EY et al. · Nature immunology 2025 · PMID 41062655 · doi:10.1038/s41590-025-02295-4

This dataset

Open GSE297597 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 GSE297597_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 PRJNA1265236 and SRA study SRP586379. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41062655) ↗

Study design

4 × D3 TIR1 vs 4 × D3 WT vs 3 × D7 TIR1 vs 3 × D7 WT

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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

GSM8995463 D3 TIR1 rep1 D3 TIR1
GSM8995464 D3 WT rep1 D3 WT
GSM8995465 D3 WT rep2 D3 WT
GSM8995466 D3 TIR1 rep2 D3 TIR1
GSM8995467 D3 WT rep3 D3 WT
GSM8995468 D3 TIR1 rep3 D3 TIR1
GSM8995469 D3 WT rep4 D3 WT
GSM8995470 D3 TIR1 rep4 D3 TIR1
GSM8995471 D7 TIR1 rep1 D7 TIR1
GSM8995472 D7 WT rep1 D7 WT
GSM8995473 D7 WT rep2 D7 WT
GSM8995474 D7 WT rep3 D7 WT
GSM8995475 D7 TIR1 rep2 D7 TIR1
GSM8995476 D7 TIR1 rep3 D7 TIR1

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