GEO series

REV-ERBα regulates regulatory T cell function in inflammatory bowel disease [CUT&RUN]

GSE225202 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 29 samples Submitted 2025/11/10 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 29 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: 29 samples: 29 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)

Colonic Rorgt+Foxp3+ Treg cells are critical to maintain intestinal homeostasis and prevent inflammatory bowel diseases by suppressing exuberant innate and adaptative immune responses. In this study, In this study, we found that REV-ERB was highly expressed in colonic RORt+Foxp3+ Treg cells and essential for their differentiation and function.

Read the full summary ↓

Deletion of REV-ERB in Treg cells lead to diminished colonic RORt+Foxp3+ Treg cell populations even at steady state, and render mice more susceptible to TNBS and/or oxazolone-induced colitis. As a transcriptional repressor, REV-ERB can directly repress the expression of pro-inflammatory cytokines IL-17a and IL-17f, and promote RORt expression through Bhlhe40-c-maf axis in RORt+Foxp3+ Treg cells. Furthermore, REV-ERB also orchestrate RORt genome-wide distributions and co-regulate core signature genes in RORt+Foxp3+ Treg cells, including IL-10, CTLA-4, Icos, c-maf.

This dataset

Open GSE225202 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 GSE225202_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 PRJNA934503 and SRA study SRP422550. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

29 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 29 sample titles: 29 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

GSM7041361 REVERB KO Treg, Foxp3
GSM7041362 REVERB KO Treg, H3K27AC
GSM7041363 REVERB KO Treg, normal IgG control
GSM7041364 REVERB KO Treg, RORgt
GSM7041365 REVERB KO Treg, REVERBa
GSM7041366 REVERB WT Treg, Foxp3
GSM7041367 REVERB WT Treg, H3K27AC
GSM7041368 REVERB WT Treg, normal IgG control
GSM7041369 REVERB WT Treg, RORgt
GSM7041370 REVERB WT Treg, REVERBa
GSM7041371 REVERB WT Treg, H3K27ac2D1
GSM7041372 REVERB WT Treg, normal IgGD1 control
GSM7041373 REVERB WT Treg, REVERBaD5
GSM7041374 REVERB WT Treg, retroviral vector, IgG control
GSM7041375 REVERB WT Treg, retroviral vector, RORgt
GSM7041376 REVERB WT Treg, transduced with RORc, IgG control
GSM7041377 REVERB WT Treg, transduced with RORc, RORgt
GSM7041378 REVERB KO Treg, retroviral vector, IgG control
GSM7041379 REVERB KO Treg, retroviral vector, RORgt
GSM7041380 REVERB KO Treg, transduced with RORc, IgG control
GSM7041381 REVERB KO Treg, transduced with RORc, RORgt
GSM7041382 REVERB KO Treg, DEC1
GSM7041383 REVERB KO Treg, IgG control for DEC1
GSM7041384 REVERB WT Treg, DEC1
GSM7041385 REVERB WT Treg, IgG control for DEC1
GSM7041386 REVERB KO Treg, c-maf
GSM7041387 REVERB KO Treg, IgG control for c-maf
GSM7041388 REVERB WT Treg, c-maf
GSM7041389 REVERB WT Treg, IgG control for c-maf

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