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Developmentally dynamic chromatin state at loci regulating interorgan communication

GSE295997 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 96 samples Submitted 2025/12/31 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 96 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
96 samples: 24 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
Developmentally dynamic chromatin state at loci regulating organ crosstalk by remote sensing and signalingEpigenetics & chromatin · 2025
Summary (written by the submitters)
Interorgan communication, metabolite regulation and drug handling all require fine-tuned transport of small molecules across cellular membranes. Approximately 1000 protein-coding genes – including hundreds of solute carrier (SLC) and ATP-binding cassette (ABC) transporters as well as enzymes and transcription factors-mediate small molecule organ crosstalk via a process known as “remote sensing and signaling (RSS)”.
Read the full summary ↓
The RSS protein coding genes greatly overlap with those regulating absorption, digestion, metabolism and excretion (ADME) of small molecule drugs. However, it is not known how chromatin and epigenetic state at these loci are coordinately regulated during the development of the liver and kidney, which control the small molecule composition of the blood, or the brain, whose physiology relies upon proper regulation of this process. Understanding how epigenetic state changes during development at these loci provides insight into how the body attains autonomous functionality.
Published in
Developmentally dynamic chromatin state at loci regulating organ crosstalk by remote sensing and signaling
Parmar A, Nigam SK, Cai K et al. · Epigenetics & chromatin 2025 · PMID 41340067 · doi:10.1186/s13072-025-00648-9
This dataset
Open GSE295997 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 GSE295997_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 PRJNA1257285 and SRA study SRP583176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41340067) ↗
Study design
24 conditions, mostly with about 4 replicates each
Brain, embryonic day 16, H3K4me3, ×4 Brain, adult (3 months), H3K4me3, ×4 Brain, embryonic day 16, H3K9ac, ×4 Brain, adult (3 months), H3K9ac, ×4 Brain, embryonic day 16, H3K27ac, ×4 Brain, adult (3 months), H3K27ac, ×4 Brain, embryonic day 16, H3K27me3, ×4 Brain, adult (3 months), H3K27me3, ×4 +16 more

Supports a between-group comparison across 96 samples.

How we read this: 24 replicated groups read from 96 sample titles; they account for 96 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

+ 56 more — browse all 96 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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