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The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis.

GSE274495 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 421 samples Submitted 2025/07/23 Platform GPL24676Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 421 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
421 samples: 143 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
Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesisNature cell biology · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE274495 in finder → Find more RNA-seq 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 GSE274495_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 PRJNA1146730 and SRA study SRP525583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41034520) ↗
Study design
143 conditions, mostly in triplicate
WT_RNA-TGC-5.5_invitro ×4 WT_RNA-Epi-4.5 ×3 WT_RNA-Epi-4.75 ×3 WT_RNA-Epi-5.0_invivo ×3 WT_RNA-Epi-5.0 ×3 WT_RNA-Epi-5.25_invivo ×3 WT_RNA-Epi-5.25 ×3 WT_RNA-Epi-5.5_invitro ×3 +168 more

Supports a between-group comparison across 367 samples.

How we read this: 143 replicated groups read from the first 400 of 421 sample titles; they account for 367 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

+ 381 more — browse all 421 samples with per-sample file links →

Datasets on a similar topic

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