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ChIPseq - Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes

GSE293134 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 39 samples Submitted 2026/03/17 Platform GPL24676Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 39 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
Homo sapiens (human)
Samples
39 samples: 14 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
Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytesCommunications biology · 2026
Summary (written by the submitters)
Epigenetic regulation is a key determinant of adipocyte fate and function, conferring phenotypic plasticity to adipose tissue in response to metabolic and thermal challenges. To understand the spatiotemporal regulation of chromatin during the establishment of a beige thermogenic adipocyte phenotype, we analyzed the transcriptomic, epigenetic, and enhancer connectome dynamics during white and beige adipogenesis.
Read the full summary ↓
Using a machine learning approach, we find that the white-specific transcriptional program is associated with promoter modulations of H3K2ac levels and chromatin accessibility. In contrast, beige-specific mitochondrial gene expression correlates with promoter changes in H3K4me3 levels. Adipocyte beiging is also mediated by a remodeling of the 3D genome involving the recruitment of short range enhancers targeting fatty acid oxidation and thermogenic genes. These increased promoter-enhancer contacts correlate with increased chromatin opening at sites enriched for C/EBP transcription factor motifs. We notably identify the C/EBP transcription factor NFIL3 as differentially bound between white and beige adipocytes at enhancers regulating PDK4, a key metabolic switch promoting fatty acid oxidation. Our results highlight a multimodal, pathway-specific regulation of the transcriptional program underlying the beige adipocyte phenotype.
Published in
Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes
Hazell Pickering S, Galigniana NM, Abdelhalim M et al. · Communications biology 2026 · PMID 41501500 · doi:10.1038/s42003-025-09469-8
This dataset
Open GSE293134 in finder → Find more human 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 GSE293134_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 PRJNA1242864 and SRA study SRP573674. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41501500) ↗
Study design
14 conditions, mostly in duplicate
beige_H3K36me3_D ×3 beige_H3K9me3_D ×3 white_H3K36me3_D ×3 white_H3K9me3_D ×3 beige_H3K27ac_D ×2 beige_H3K27me3_D ×2 beige_H3K4me1_D ×2 beige_H3K4me3_D ×2 +13 more

Supports a between-group comparison across 32 samples.

How we read this: 14 replicated groups read from 39 sample titles; they account for 32 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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