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Interplay between Genetic Variation and Nutrition Challenge Controls Hepatic Diurnal Rhythms [ChIP-seq]

GSE278921 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2025/08/25 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
13 samples: 3 × B6, Liver,NC,EsrrgChIP-seq, vs 3 × B6, Liver,HFD,EsrrgChIP-seq, vs 3 × S129,liver,NC,EsrrgChIP-seq, vs 3 × S129,liver,HFD,EsrrgChIP-seq,Groups 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
Genetics-nutrition interactions control diurnal enhancer-promoter dynamics and liver lipid metabolismCell metabolism · 2025
Summary (written by the submitters)
Variation in diurnal rhythms contributes to the risk of multiple diseases, yet the genomic and epigenomic basis remains largely unknown. Here, we show that SNPs in enhancer and promoter regions genome-wide contribute to variations in human diurnal rhythms. Differential rhythmic gene expression and physiological responses to diet-induced obesity in mice with different genetic backgrounds are linked to time-dependent enhancer-promoter interactions (EPI) regulated by cis-regulatory SNPs and transcription factors (TFs) like ESRRγ.
Read the full summary ↓
Hepatocyte-specific Esrrγ knockout alters rhythmic processes in liver, including triglyceride synthesis and lipid droplet formation, across mouse strains. Moreover, motifs of ESRRγ and other lipid metabolism-related TFs are enriched in individual-specific EPIs harboring SNPs to control rhythmic genes in patients with MAFLD. SNPs located in these sites are correlated with hepatic metabolic traits. Thus, SNPs and TFs interdependently form the genomic and epigenomic basis for diurnal rhythm variation, contributing to disease risk.
Published in
Genetics-nutrition interactions control diurnal enhancer-promoter dynamics and liver lipid metabolism
Zhou D, Chen Y, Liu P et al. · Cell metabolism 2025 · PMID 40858101 · doi:10.1016/j.cmet.2025.07.010
This dataset
Open GSE278921 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 GSE278921_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 PRJNA1169621 and SRA study SRP536899. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40858101) ↗
Study design
3 × B6, Liver,NC,EsrrgChIP-seq, vs 3 × B6, Liver,HFD,EsrrgChIP-seq, vs 3 × S129,liver,NC,EsrrgChIP-seq, vs 3 × S129,liver,HFD,EsrrgChIP-seq,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 13 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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