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Dynamic promoter-enhancer contacts contribute to spatiotemporal gene expression during mouse fetal development

GSE200114 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 70 samples Submitted 2024/09/02 Platform GPL24247Platform GPL21103Platform GPL17021Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 70 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
70 samples: 34 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
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissuesNature structural & molecular biology · 2025
Summary (written by the submitters)
While a rich set of putative cis-regulatory sequences involved in mouse fetal development has been annotated recently based on chromatin accessibility and histone modification patterns, delineating their roles in developmentally regulated gene expression continues to be challenging due to a lack of information regarding their putative target genes.
Read the full summary ↓
To fill this gap, we examined the tissue-to-tissue variability and developmental dynamics of chromatin contacts between gene promoters and distal sequences genome-wide in mouse embryos. Among the 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes, many occur between promoters and putative enhancers located hundreds of kilobases away. More than 75% of the chromatin interactions coincide with the binding of CTCF at one or both anchors, underscoring a broad role for this chromatin organizer in developmentally regulated 3D chromatin conformation. The predicted target genes of 15,098 candidate enhancers demonstrate highly tissue-specific and developmental stage restricted expression patterns, and may facilitate the annotation of noncoding risk variants associated with human diseases.
Published in
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues
Yu M, Zemke NR, Chen Z et al. · Nature structural & molecular biology 2025 · PMID 39681766 · doi:10.1038/s41594-024-01431-2
This dataset
Open GSE200114 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 GSE200114_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 PRJNA823013 and SRA study SRP367482. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39681766) ↗
Study design
34 conditions, mostly in duplicate
H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 12.5 day mouse … ×2 H3K4me3 PLAC-seq on embryonic 13.5 day mouse … ×2 +28 more

Supports a between-group comparison across 68 samples.

How we read this: 34 replicated groups read from 70 sample titles; they account for 68 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

+ 30 more — browse all 70 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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