GEO series

Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [ChIP-seq]

GSE267320 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2025/07/22 Platform GPL21103

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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: 20 samples: 10 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: Early-life ketone body signalling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylomeNature metabolism · 2025

Summary (written by the submitters)

Infants experience distinct ketogenesis during the preweaning period, but its physiological significance remains unclear. Here, we show that preweaning ketosis enhances beige fat biogenesis and improves metabolic health in adulthood. To elucidate the underlying mechanisms, we performed multi-omics analyses of inguinal white adipose tissue (iWAT) and its stromal vascular fraction (SVF).

Read the full summary ↓

Bulk RNA-seq of iWAT was conducted in 8-week-old Hmgcs2 knockout (KO) and control mice housed at room temperature (23 °C) or exposed to cold (4 °C). To further examine the effects of elevated ketosis, we administered oral 1,3-butanediol (1,3BD) or water to pups from postnatal day 2 to 21, and analyzed the iWAT SVF using bulk RNA-seq, single-cell RNA-seq, and ChIP-seq targeting H3K9ac, H3K14ac, and H3K9bhb. These integrative analyses reveal how early-life ketosis programs adipose progenitors to promote beige adipocyte development.

Published in

Early-life ketone body signalling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome

Jiang CL, Lai PH, Yang PC et al. · Nature metabolism 2025 · PMID 41068421 · doi:10.1038/s42255-025-01378-8

This dataset

Open GSE267320 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 GSE267320_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 PRJNA1111060 and SRA study SRP507355. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41068421) ↗

Study design

10 conditions, mostly in duplicate

SVF, Water, H3K9ac, ChIP ×2 SVF, Water, H3K14ac, ChIP ×2 SVF, Water, H3K9bhb, ChIP ×2 SVF, Water, input ×2 SVF, 1,3BD, H3K9ac, ChIP ×2 SVF, 1,3BD, H3K14ac, ChIP ×2 SVF, 1,3BD, H3K9bhb, ChIP ×2 SVF, 1,3BD, input ×2 +2 more

Supports a between-group comparison across 20 samples.

How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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

GSM8263874 SVF, Water, H3K9ac, ChIP_1 SVF, Water, H3K9ac, ChIP
GSM8263875 SVF, Water, H3K9ac, ChIP_2 SVF, Water, H3K9ac, ChIP
GSM8263876 SVF, Water, H3K14ac, ChIP_1 SVF, Water, H3K14ac, Ch…
GSM8263877 SVF, Water, H3K14ac, ChIP_2 SVF, Water, H3K14ac, Ch…
GSM8263878 SVF, Water, H3K9bhb, ChIP_1 SVF, Water, H3K9bhb, Ch…
GSM8263879 SVF, Water, H3K9bhb, ChIP_2 SVF, Water, H3K9bhb, Ch…
GSM8263880 SVF, Water, input_1 SVF, Water, input
GSM8263881 SVF, Water, input_2 SVF, Water, input
GSM8263882 SVF, 1,3BD, H3K9ac, ChIP_1 SVF, 1,3BD, H3K9ac, ChIP
GSM8263883 SVF, 1,3BD, H3K9ac, ChIP_2 SVF, 1,3BD, H3K9ac, ChIP
GSM8263884 SVF, 1,3BD, H3K14ac, ChIP_1 SVF, 1,3BD, H3K14ac, Ch…
GSM8263885 SVF, 1,3BD, H3K14ac, ChIP_2 SVF, 1,3BD, H3K14ac, Ch…
GSM8263886 SVF, 1,3BD, H3K9bhb, ChIP_1 SVF, 1,3BD, H3K9bhb, Ch…
GSM8263887 SVF, 1,3BD, H3K9bhb, ChIP_2 SVF, 1,3BD, H3K9bhb, Ch…
GSM8263888 SVF, 1,3BD, input_1 SVF, 1,3BD, input
GSM8263889 SVF, 1,3BD, input_2 SVF, 1,3BD, input
GSM8919684 SVF, KO, H3K9bhb, ChIP_1 SVF, KO, H3K9bhb, ChIP
GSM8919685 SVF, KO, H3K9bhb, ChIP_2 SVF, KO, H3K9bhb, ChIP
GSM8919686 SVF, KO, Input, ChIP_1 SVF, KO, Input, ChIP
GSM8919687 SVF, KO, Input, ChIP_2 SVF, KO, Input, ChIP

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GSE288332 Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions. [ATAC-Seq] 18 samples shares early-life
GSE268468 Persistent open chromatin state in early-life stress-activated cells of the VTA 10 samples shares early-life

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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.