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Circadian clocks and periodic anticipated fasting prevent fasting-associated hepatic steatosis in calorie restriction

GSE278669 Mus musculus (mouse) RNA-seq (gene expression) 38 samples Submitted 2025/07/18 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 38 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
38 samples: 13 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
Circadian clocks and periodic anticipated fasting prevent fasting-associated hepatic steatosis in calorie restrictionCell reports · 2025
Summary (written by the submitters)
Calorie restriction (CR) improves health and longevity. CR induces a periodic fasting cycle in mammals; our study compares CR with unanticipated fasting (F), when the food is unexpectedly withheld. F induces hepatic steatosis, while CR reduces it; surprisingly, the difference is not due to hepatic β-oxidation. Liver transcriptome analysis identifies fatty acid transporters (Slc27a1 and Slc27a2), TAG synthesis (Gpat4), and lipid storage (Plin2 and Cidec) genes to be upregulated only in F in agreement with hepatic steatosis.
Read the full summary ↓
The circadian clock and anticipated fasting contribute to preventing fasting-associate hepatic steatosis in CR. Mechanistically, Slc27a1, Plin2 and Cidec genes are upregulated, and liver TAGs accumulate in circadian clock mutant mice on CR or if wild type CR mice miss their anticipated meal. The results highlight similarities and differences between unanticipated fasting and CR, suggesting that circadian clock dependent gating of transcriptional response to fasting controls lipid homeostasis and prevents hepatic steatosis.
Published in
Circadian clocks and periodic anticipated fasting prevent fasting-associated hepatic steatosis in calorie restriction
Ebeigbe OP, Mezhnina V, Astafev A et al. · Cell reports 2025 · PMID 40802509 · doi:10.1016/j.celrep.2025.116141
This dataset
Open GSE278669 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 GSE278669_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 PRJNA1168174 and SRA study SRP536306. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40802509) ↗
Study design
13 conditions, mostly in triplicate
22h Calorie restriction ×4 0h Ad libitum ×3 6h Calorie restriction ×3 6h Fasted ×3 14h Ad libitum ×3 14h Calorie restriction ×3 14h Fasted ×3 22h Ad libitum ×3 +5 more

Supports a between-group comparison across 38 samples.

How we read this: 13 replicated groups read from 38 sample titles; they account for 38 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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