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Differences in mitotic chromosome organization between cell types and species

GSE249331 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2025/05/13 Platform GPL21103Platform GPL30173Platform GPL30172Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
15 samples: 6 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
Mitotic chromosomes harbor cell type- and species-specific structural features within a universal loop array conformationGenome research · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Mitotic chromosomes harbor cell type- and species-specific structural features within a universal loop array conformation
Oomen ME, Fox AN, Gonzalez I et al. · Genome research 2025 · PMID 40480831 · doi:10.1101/gr.280648.125
This dataset
Open GSE249331 in finder → Find more 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 GSE249331_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 PRJNA1048527 and SRA study SRP475730. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40480831) ↗
Study design
6 conditions, mostly in duplicate
DpnII Hi-C on asynchronous C2C12 cells ×2 DpnII Hi-C on mitotic mESCs ×2 DpnII Hi-C on asynchronous mESCs ×2 ATAC-seq on asynchronous C2C12 cells ×2 ATAC-seq on mitotic C2C12 cells ×2 DpnII Hi-C on mitotic synchronized and sorted… ×2 DpnII Hi-C on G2 synchronized HeLa cells rele… ×1 DpnII Hi-C on G2 synchronized HeLa cells rele… ×1 +1 more

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 15 sample titles; they account for 12 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
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.