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Chronic intermittent hypoxia mimicking sleep apnea reshapes the liver circadian metabolic architecture

GSE302604 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/01/16 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 36 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
36 samples: 12 conditions, mostly in triplicateGroups 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
Chronic intermittent hypoxia reshapes circadian metabolic architecture in a model of sleep apneaScience advances · 2026
Summary (written by the submitters)
Obstructive sleep apnea (OSA), characterized by chronic intermittent hypoxia (IH) during sleep, is increasingly recognized as a driver of metabolic dysfunction. However, its impact on circadian metabolic regulation remains poorly understood. Here, we investigated how chronic IH reshapes 24- hour hepatic and systemic metabolic programs in a mouse model mimicking OSA-associated hypoxia.
Read the full summary ↓
Through integrated circadian transcriptomic, metabolomic, and physiological profiling, we show that four weeks of rest phase-restricted IH reprogram hepatic metabolism in a time-specific manner. This reorganization involves the coordinated circadian regulation of glucose, lipid, and redox pathways, with a shift away from oxidative metabolism and toward oxygen-sparing processes such as gluconeogenesis, glycogen turnover, and lipid mobilization. These changes align with the hypoxic phase and coincide with altered metabolite oscillations and autonomic rhythms, supporting a functional adaptation to intermittent oxygen availability. Mechanistically, we identify rhythmic activation of the cAMP–CREB1 axis as a key transcriptional driver linking adrenergic signaling to circadian metabolic remodeling under IH. Our findings establish chronic IH as a potent metabolic zeitgeber that entrains hepatic transcriptional and metabolic rhythms, revealing a circadian dimension to the metabolic consequences of sleep-disordered breathing.
Published in
Chronic intermittent hypoxia reshapes circadian metabolic architecture in a model of sleep apnea
Montellier E, Vial G, Bouyon S et al. · Science advances 2026 · PMID 41739942 · doi:10.1126/sciadv.aeb3756
This dataset
Open GSE302604 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 GSE302604_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1291490 and SRA study SRP601173. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41739942) ↗
Study design
12 conditions, mostly in triplicate
Intermittent hypoxia - ZT0 ×3 Intermittent hypoxia - ZT4 ×3 Intermittent hypoxia - ZT8 ×3 Intermittent hypoxia - ZT12 ×3 Intermittent hypoxia - ZT16 ×3 Intermittent hypoxia - ZT20 ×3 Normoxia control - ZT0 ×3 Normoxia control - ZT4 ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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