GEO series

Deletion of a Distal IRF4 Element Prevents Inflammation-induced Reprogramming of Human Regulatory T-cell Fate

GSE331192 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2026/08/03 Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 22 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: Homo sapiens (human)
Samples: 22 samples: 22 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

Adoptive regulatory T cell (Treg) therapy is an emergent treatment paradigm for restoring immune tolerance in patients with autoimmune and inflammatory diseases. While preclinical models have demonstrated the remarkable efficacy of Treg cell therapy, lineage-tracing studies have also revealed that murine Tregs can lose lineage identity and adopt a proinflammatory state.

Read the full summary ↓

Whether human Tregs exhibit a similar susceptibility to inflammatory cytokine-mediated lineage decommitment remains inconclusive. Here, we present an in vitro model of human Treg destabilization characterized by silencing of the Treg lineage-defining transcription factor, FOXP3, loss of suppressive activity, and gain of proinflammatory functions. Analysis of single-cell ATAC and transcriptomic profiles of Tregs during destabilization revealed a switch in chromatin accessibility between two elements at the IRF4 locus. Excision of the distal IRF4 element enabled Tregs to resist inflammatory cytokine-induced reprogramming, presenting a cell-engineering strategy to design more effective Treg therapies.

This dataset

Open GSE331192 in finder → Find more human 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 GSE331192_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 PRJNA1467466 and SRA study SRP701517. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

22 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 22 sample titles: 22 distinct titles with little repetition. 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

GSM9741489 Regulatory T cells, donor 1104, condition C, ATAC-seq
GSM9741491 Regulatory T cells, donor 1104, condition 1B, ATAC-seq
GSM9741492 Regulatory T cells, donor 1104, condition 6, ATAC-seq
GSM9741493 Regulatory T cells, donor 1104, condition 23, ATAC-seq
GSM9741494 Regulatory T cells, donor 1104, condition A, ATAC-seq
GSM9741495 Regulatory T cells, donor 4980, condition C, ATAC-seq
GSM9741497 Regulatory T cells, donor 4980, condition 1B, ATAC-seq
GSM9741498 Regulatory T cells, donor 4980, condition 6, ATAC-seq
GSM9741499 Regulatory T cells, donor 4980, condition 23, ATAC-seq
GSM9741500 Regulatory T cells, donor 4980, condition A, ATAC-seq
GSM9741501 Regulatory T cells, donor 7570, condition C, ATAC-seq
GSM9741503 Regulatory T cells, donor 7570, condition 1B, ATAC-seq
GSM9741504 Regulatory T cells, donor 7570, condition 6, ATAC-seq
GSM9741505 Regulatory T cells, donor 7570, condition A, ATAC-seq
GSM9741506 Regulatory T cells, donor 8341, condition C, ATAC-seq
GSM9741508 Regulatory T cells, donor 8341, condition 1B, ATAC-seq
GSM9741510 Regulatory T cells, donor 8341, condition 23, ATAC-seq
GSM9741511 Regulatory T cells, donor 8341, condition A, ATAC-seq
GSM9741512 Conventional T cells, donor 1104, condition TC, ATAC-seq
GSM9741513 Conventional T cells, donor 4980, condition TC, ATAC-seq
GSM9741514 Conventional T cells, donor 7570, condition TC, ATAC-seq
GSM9741515 Conventional T cells, donor 8341, condition TC, ATAC-seq

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