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The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag]

GSE274493 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 46 samples Submitted 2025/07/24 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 46 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
46 samples: 20 conditions, mostly in duplicateGroups 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
Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesisNature cell biology · 2025
Summary (written by the submitters)
Since its discovered, the dynamics and molecular regulation of bivalent chromatin during early embryogenesis remain poorly understood. We trace gene expression and bivalent chromatin dynamics in peri-implantation mouse embryogenesis, showing bifurcated establishment in epiblast and primitive endoderm. We identify transiently maintained bivalent domains (TB domains) in the epiblast, crucial for pluripotency progression.
Read the full summary ↓
Our study reveals 22 candidate factors, including ZBTB17, essential for resolving TB domains and activating pluripotency regulators. These dynamics are conserved in human pluripotent transition.
Published in
Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesis
Li Y, He J, Liu Y et al. · Nature cell biology 2025 · PMID 41034520 · doi:10.1038/s41556-025-01776-w
This dataset
Open GSE274493 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 GSE274493_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 PRJNA1146737 and SRA study SRP525583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41034520) ↗
Study design
20 conditions, mostly in duplicate
Valid_EB_CT-EB_ZbHA_Eed-d3-CUT&Tag ×2 Valid_EB_CT-EB_ZbHA_H3K27me3-d3-CUT&Tag ×2 Valid_EB_CT-EB_ZbHA_H3K4me3-d3-CUT&Tag ×2 Valid_EB_CT-EB_ZbKO_Eed-d3-CUT&Tag ×2 Valid_EB_CT-EB_ZbKO_H3K27me3-d3-CUT&Tag ×2 Valid_EB_CT-EB_ZbKO_H3K4me3-d3-CUT&Tag ×2 Valid_GSK_CT-Epi_Gsk_H3K27me3-5.0-CUT&Tag ×2 Valid_GSK_CT-Epi_WT_H3K27me3-5.0-CUT&Tag ×2 +18 more

Supports a between-group comparison across 40 samples.

How we read this: 20 replicated groups read from 46 sample titles; they account for 40 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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