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EOMES safeguards TSC chromatin accessibility by directing BRG1 to TSC-associated loci [ATAC-seq]

GSE276039 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2025/05/19 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 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
36 samples
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
Eomesodermin in conjunction with the BAF complex promotes expansion and invasion of the trophectoderm lineageNature communications · 2025
Summary (written by the submitters)
EOMES is an essential transcription factor (TF) for murine trophoblast stem cell (TSC) maintenance. Despite that, the details of EOMES' function at the molecular level remain obscure. Here, we carried out rapid immunoprecipitation and mass spectrometry of endogenous protein (RIME) to identify TSC-specific protein interactors on EOMES.
Read the full summary ↓
In addition to other established TFs involved in TSC maintenance, we found that EOMES interacts with several chromatin remodeller subunits, including BRG1. By exploiting an Eomes-degron system, we acutely depleted EOMES protein in TSCs and in parallel inhibited BRG1 function with small molecule BRM014. EOMES depletion and BRG1 inhibition resulted in reduced accessibility at largely overlapping genomic regions associated with TSC-related loci. Additionally, EOMES depletion results in misregulation of genes essential for TSC maintenance and function, as well as genes encoding cytoskeletal, cell-cell interaction and matricellular components.
Published in
Eomesodermin in conjunction with the BAF complex promotes expansion and invasion of the trophectoderm lineage
Bisia AM, Xypolita ME, Bikoff EK et al. · Nature communications 2025 · PMID 40450029 · doi:10.1038/s41467-025-60417-w
This dataset
Open GSE276039 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 GSE276039_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 PRJNA1154562 and SRA study SRP529593. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40450029) ↗
Samples in this study

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+ 36 more — browse all 36 samples with per-sample file links →

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