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Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [Foxp3-AID-14D RNA-seq]

GSE302585 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/08/28 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 10 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: 10 samples: 6 × Tir1 vs 4 × 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 GSE302585 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 GSE302585_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 PRJNA1291242 and SRA study SRP600775. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41062655) ↗

Study design

6 × Tir1 vs 4 × WT

Supports a between-group comparison across 10 samples.

How we read this: 2 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

GSM9107028 WT.rep1 WT
GSM9107029 WT.rep2 WT
GSM9107030 WT.rep3 WT
GSM9107031 WT.rep4 WT
GSM9107032 Tir1.rep5 Tir1
GSM9107033 Tir1.rep6 Tir1
GSM9107034 Tir1.rep7 Tir1
GSM9107035 Tir1.rep8 Tir1
GSM9107036 Tir1.rep9 Tir1
GSM9107037 Tir1.rep10 Tir1

Datasets on a similar topic

GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares foxp3, transcription, regulatory
GSE267967 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq] 26 samples shares foxp3, regulatory
GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples shares foxp3, regulatory
GSE229592 Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity 32 samples shares foxp3, transcription
GSE267884 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [scMultiome] 16 samples shares foxp3, regulatory
GSE251931 Maintenance of tolerance after lung transplantation is dependent on the preservation of allograft tissue-resident Foxp3+ T cells 15 samples shares foxp3, maintenance
GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription, maintenance
GSE329967 Temporal Single-Cell Transcriptional Dynamics of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression 33 samples shares transcription, temporal

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.