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The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function [C2C12]

GSE308278 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/01/14 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × C2C12 w/ WT ZT4 serum vs 4 × C2C12 w/ Bmal1hep-/- ZT4 serum vs 4 × C2C12 w/ WT ZT16 serum vs 4 × C2C12 w/ Bmal1hep-/- ZT16 serumGroups 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
The Liver Clock Tunes Transcriptional Rhythms in Skeletal Muscle to Regulate Mitochondrial FunctionJournal of biological rhythms · 2026
Summary (written by the submitters)
Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis, yet the specific inter-organ signalling axes involved are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet the impact of the liver clock on the muscle remains unknown.
Read the full summary ↓
Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) to reveal that approximately one-third of transcript rhythms in skeletal muscle are influenced by the liver clock in vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibits expression of genes involved in metabolic pathways, including oxidative phosphorylation. Only small transcriptional changes were induced by liver clock–driven endocrine communication in vitro, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Consistent with functional tuning, treatment of myotubes with serum collected from Bmal1hep-/- mice during the dark phase lowers mitochondrial ATP production as compared to serum from wild-type mice. Overall, our results reveal communication between the liver clock and skeletal muscle, uncovering a bidirectional endocrine communication pathway that may contribute to the metabolic phenotypes of circadian disruption.
Published in
The Liver Clock Tunes Transcriptional Rhythms in Skeletal Muscle to Regulate Mitochondrial Function
Sica V, Sato T, Tsialtas I et al. · Journal of biological rhythms 2026 · PMID 41486525 · doi:10.1177/07487304251386926
This dataset
Open GSE308278 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 GSE308278_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 PRJNA1330046 and SRA study SRP620964. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41486525) ↗
Study design
4 × C2C12 w/ WT ZT4 serum vs 4 × C2C12 w/ Bmal1hep-/- ZT4 serum vs 4 × C2C12 w/ WT ZT16 serum vs 4 × C2C12 w/ Bmal1hep-/- ZT16 serum

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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