GEO series

Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle

GSE290224 Mus musculus (mouse) Single-cell RNA-seq 96 samples Submitted 2026/03/18 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 96 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 96 samples: 12 conditions, mostly with about 8 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: Uncovering shared and tissue-specific molecular adaptations to intermittent fasting in liver, brain, and muscleeLife · 2026

Summary (written by the submitters)

Intermittent fasting (IF), a dietary regimen that mimics the natural feeding patterns observed across diverse organisms—from single-celled life to mammals—is thought to activate systemic survival responses and confer health benefits. However, the molecular mechanisms underlying these effects remain poorly understood. In this study, we utilized ATAC-Seq and RNA-Seq to investigate how IF influences chromatin accessibility and gene expression in brain and muscle tissues of mice, compared to ad libitum feeding.

Read the full summary ↓

Our results reveal that IF induces significant changes in chromatin accessibility, modulating pathways related to metabolism, ribosome function, HIF-1 signaling, and glycolysis. Motif analysis identified tissue-specific transcription factors enriched in IF-regulated regions, including Sp1, Mef2a, NeuroD2, Banp, and NFIA in the brain, and SMAD4, TCF4, STAT5B, NKX3-1, and ZEB2 in muscle. Integrative analysis of ATAC-Seq and RNA-Seq data demonstrated that IF upregulates 50 genes and downregulates 15 in the cortex, while upregulating 31 genes and downregulating 10 in muscle. These gene expression changes are linked to pathways associated with neuroprotection and enhanced muscle function, offering mechanistic insights into the health benefits of IF. Our findings underscore the role of IF-induced chromatin remodeling in driving adaptive gene regulation.

Published in

Uncovering shared and tissue-specific molecular adaptations to intermittent fasting in liver, brain, and muscle

Fan Y, De Silva S, Tabassum NI et al. · eLife 2026 · PMID 41995076 · doi:10.7554/eLife.107332

This dataset

Open GSE290224 in finder → Find more mouse RNA-seq 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 GSE290224_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1226611 and SRA study SRP565540. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41995076) ↗

Study design

12 conditions, mostly with about 8 replicates each

Cortex,Ad_libtum,Male, ×8 Cortex,Intermittent_fasting,Male, ×8 Cortex,Ad_libtum,Female, ×8 Cortex,Intermittent_fasting,Female, ×8 Liver,Ad_libtum,Male, ×8 Liver,Intermittent_fasting,Male, ×8 Liver,Ad_libtum,Female, ×8 Liver,Intermittent_fasting,Female, ×8 +4 more

Supports a between-group comparison across 96 samples.

How we read this: 12 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

GSM8808701 Cortex,Ad_libtum,Male,rep1 Cortex,Ad_libtum,Male,
GSM8808702 Cortex,Ad_libtum,Male,rep2 Cortex,Ad_libtum,Male,
GSM8808703 Cortex,Ad_libtum,Male,rep3 Cortex,Ad_libtum,Male,
GSM8808704 Cortex,Ad_libtum,Male,rep4 Cortex,Ad_libtum,Male,
GSM8808705 Cortex,Ad_libtum,Male,rep5 Cortex,Ad_libtum,Male,
GSM8808706 Cortex,Ad_libtum,Male,rep6 Cortex,Ad_libtum,Male,
GSM8808707 Cortex,Ad_libtum,Male,rep7 Cortex,Ad_libtum,Male,
GSM8808708 Cortex,Ad_libtum,Male,rep8 Cortex,Ad_libtum,Male,
GSM8808709 Cortex,Intermittent_fasting,Male,rep1 Cortex,Intermittent_fas…
GSM8808710 Cortex,Intermittent_fasting,Male,rep2 Cortex,Intermittent_fas…
GSM8808711 Cortex,Intermittent_fasting,Male,rep3 Cortex,Intermittent_fas…
GSM8808712 Cortex,Intermittent_fasting,Male,rep4 Cortex,Intermittent_fas…
GSM8808713 Cortex,Intermittent_fasting,Male,rep5 Cortex,Intermittent_fas…
GSM8808714 Cortex,Intermittent_fasting,Male,rep6 Cortex,Intermittent_fas…
GSM8808715 Cortex,Intermittent_fasting,Male,rep7 Cortex,Intermittent_fas…
GSM8808716 Cortex,Intermittent_fasting,Male,rep8 Cortex,Intermittent_fas…
GSM8808717 Cortex,Ad_libtum,Female,rep1 Cortex,Ad_libtum,Female,
GSM8808718 Cortex,Ad_libtum,Female,rep2 Cortex,Ad_libtum,Female,
GSM8808719 Cortex,Ad_libtum,Female,rep3 Cortex,Ad_libtum,Female,
GSM8808720 Cortex,Ad_libtum,Female,rep4 Cortex,Ad_libtum,Female,
GSM8808721 Cortex,Ad_libtum,Female,rep5 Cortex,Ad_libtum,Female,
GSM8808722 Cortex,Ad_libtum,Female,rep6 Cortex,Ad_libtum,Female,
GSM8808723 Cortex,Ad_libtum,Female,rep7 Cortex,Ad_libtum,Female,
GSM8808724 Cortex,Ad_libtum,Female,rep8 Cortex,Ad_libtum,Female,
GSM8808725 Cortex,Intermittent_fasting,Female,rep1 Cortex,Intermittent_fas…
GSM8808726 Cortex,Intermittent_fasting,Female,rep2 Cortex,Intermittent_fas…
GSM8808727 Cortex,Intermittent_fasting,Female,rep3 Cortex,Intermittent_fas…
GSM8808728 Cortex,Intermittent_fasting,Female,rep4 Cortex,Intermittent_fas…
GSM8808729 Cortex,Intermittent_fasting,Female,rep5 Cortex,Intermittent_fas…
GSM8808730 Cortex,Intermittent_fasting,Female,rep6 Cortex,Intermittent_fas…
GSM8808731 Cortex,Intermittent_fasting,Female,rep7 Cortex,Intermittent_fas…
GSM8808732 Cortex,Intermittent_fasting,Female,rep8 Cortex,Intermittent_fas…
GSM8808733 Liver,Ad_libtum,Male,rep1 Liver,Ad_libtum,Male,
GSM8808734 Liver,Ad_libtum,Male,rep2 Liver,Ad_libtum,Male,
GSM8808735 Liver,Ad_libtum,Male,rep3 Liver,Ad_libtum,Male,
GSM8808736 Liver,Ad_libtum,Male,rep4 Liver,Ad_libtum,Male,
GSM8808737 Liver,Ad_libtum,Male,rep5 Liver,Ad_libtum,Male,
GSM8808738 Liver,Ad_libtum,Male,rep6 Liver,Ad_libtum,Male,
GSM8808739 Liver,Ad_libtum,Male,rep7 Liver,Ad_libtum,Male,
GSM8808740 Liver,Ad_libtum,Male,rep8 Liver,Ad_libtum,Male,

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

GSE273878 Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq] 48 samples shares reprograms, muscle
GSE267688 Autism-associated mutations in Kdm6b affect its role as a chromatin regulator in brain development 20 samples shares chromatin, brain
GSE319252 Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [mouse_brain_OnurE_RNA-seq] 12 samples shares reprograms, brain
GSE320350 Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling 12 samples shares chromatin, fasting
GSE271791 Intermittent fasting alleviates photoreceptor degeneration and retina inflammation in oxidative stress-induced model of Age-Related Macular Degeneration 12 samples shares intermittent, fasting
GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares accessibility, chromatin
GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares chromatin, brain
GSE216371 A single-cell atlas of chromatin accessibility in mouse organogenesis 68 samples shares accessibility, chromatin

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.