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Establishment of nuclear organization in mouse embryos is regulated by multiple and redundant epigenetic pathways.

GSE244496 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 183 samples Submitted 2025/04/10 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 183 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
183 samples: 51 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)
How the pillars of nuclear organization are first established during development is not fully understood at the molecular level. Here, we investigated one of the foundations of nuclear organization, the lamina-associated domains (LADs) and undertook a screening to identify the molecular pathways regulating LAD establishment in vivo, in early mouse embryos.
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 GSE244496 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 GSE244496_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 PRJNA1023270 and SRA study SRP464255. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40273908) ↗
Study design
51 conditions, mostly with about 4 replicates each
Suv39h1_DBA_Lamin_Zygote ×5 PoolB_DBA_Lamin_Zygote ×4 PoolF_DBA_Lamin_Zygote ×4 PoolG_DBA_Lamin_Zygote ×4 PoolH_DBA_Lamin_Zygote ×4 PoolI_DBA_Lamin_Zygote ×4 PoolJ_DBA_Lamin_Zygote ×4 PoolK_DBA_Lamin_Zygote ×4 +43 more

Supports a between-group comparison across 183 samples.

How we read this: 51 replicated groups read from 183 sample titles; they account for 183 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

+ 143 more — browse all 183 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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