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Low-input genomics screening reveals epigenetic pathways that orchestrate nuclear organization in early mouse embryos.

GSE278721 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 288 samples Submitted 2025/04/10 Platform GPL24247Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 288 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
288 samples: 70 conditions, mostly with about 4 replicates eachGroups 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 establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathwaysCell · 2025
Summary (written by the submitters)
The three-dimensional folding of the genome within the nuclear space is fundamental for regulating various DNA-related processes. How nuclear organization is first established during development is not understood at the molecular level. The formation of lamina-associated domains (LADs) at the nuclear periphery represents the earliest feature of nuclear organization.
Read the full summary ↓
In this study, we conducted a screening to investigate the molecular mechanisms regulating LAD establishment in vivo, using mouse embryos. Our findings identify histone methylation pathways that cause severe disruption of nuclear architecture in early embryos. This research provides an unprecedented resource for understanding the molecular basis of nuclear organization establishment highlighting the hierarchical relationships between chromatin pathways during epigenome formation and allows for interrogation of its impact at the onset of mammalian development. This SuperSeries is composed of the SubSeries listed below.
Published in
The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways
Pal M, Schauer T, Burton A et al. · Cell 2025 · PMID 40273908 · doi:10.1016/j.cell.2025.03.044
This dataset
Open GSE278721 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 GSE278721_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 PRJNA1168513 and SRA study SRP536423. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40273908) ↗
Study design
70 conditions, mostly with about 4 replicates each
mGFP_Control_Collection1_embryo ×8 PoolJ_Collection1_embryo ×8 PoolM_Collection1_embryo ×8 mGFP_Control_Collection2_embryo ×8 PoolJ_Collection2_embryo ×8 PoolM_Collection2_embryo ×8 mGFP_Control_Collection3_embryo ×7 PoolI_Collection3_embryo ×7 +62 more

Supports a between-group comparison across 288 samples.

How we read this: 70 replicated groups read from 288 sample titles; they account for 288 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

+ 248 more — browse all 288 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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