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Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development [ATACseq]

GSE277646 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/06/01 Platform GPL21626
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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 gene regulatory landscape driving mouse gonadal supporting cell differentiationScience advances · 2025
Summary (written by the submitters)
Identifying cis-regulatory elements is essential for understanding how gene expression is precisely controlled during critical biological processes like sex determination. In this study, we aimed to uncover the cis-regulatory regions involved in the differentiation of supporting cells as Sertoli cells or pre-granulosa cells in the mouse gonads.
Read the full summary ↓
To achieve this, we combined ATAC sequencing (ATAC-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) of purified supporting cells at four developmental stages in both sexes. ATAC-seq enabled us to capture sexual and temporal changes in gene expression during cell differentiation, while ATAC-seq provided insight into chromatin accessibility, pinpointing regulatory regions that control these expression patterns. By integrating these two datasets, we identified specific cis-regulatory elements that likely guide the fate of supporting cells. Our findings shed light on the complex gene regulatory networks involved in sex fate differentiation, highlighting the critical role of cis-regulatory elements in orchestrating this process. These insights may also have implications for understanding disorders of sexual development (DSDs).
Published in
The gene regulatory landscape driving mouse gonadal supporting cell differentiation
Stévant I, Abberbock E, Ridnik M et al. · Science advances 2025 · PMID 40712010 · doi:10.1126/sciadv.adv1885
This dataset
Open GSE277646 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 GSE277646_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 PRJNA1163275 and SRA study SRP533818. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40712010) ↗
Study design
8 conditions, mostly in triplicate
ATACseq, E11.5, sorted pre-granulosa cells, T… ×3 ATACseq, E12.5, sorted pre-granulosa cells, T… ×3 ATACseq, E13.5, sorted pre-granulosa cells, T… ×3 ATACseq, E15.5, sorted pre-granulosa cells, T… ×3 ATACseq, E11.5, sorted Sertoli cells, SOX9-IR… ×3 ATACseq, E12.5, sorted Sertoli cells, SOX9-IR… ×3 ATACseq, E13.5, sorted Sertoli cells, SOX9-IR… ×3 ATACseq, E15.5, sorted Sertoli cells, SOX9-IR… ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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