GEO series

A high-resolution, sex-stratified atlas of transcriptional and alternative splicing dynamics in the fasting mouse liver.

GSE328655 Mus musculus (mouse) RNA-seq (gene expression) 80 samples Submitted 2026/04/28 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 80 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: 80 samples: 80 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

The liver's response to fasting is a fundamental adaptive mechanism, yet its temporal complexity, circadian dimension and sexual dimorphism remain incompletely understood. Here we present a high-resolution transcriptomic atlas of the fasting mouse liver, profiling both male and female C57BL/6 mice every 4 hours across a 36-hour fast initiated at a defined circadian time.

Read the full summary ↓

Using an integrated framework combining high-resolution time-series analysis with stringent statistical filtering, we identify 2,995 genes organised into eight kinetically distinct clusters that collectively delineate a phased transcriptional transition from acute metabolic remodelling to prolonged nutrient deprivation. Contrary to prior reports, fasting amplifies rather than diminishes circadian transcription, increasing the number of rhythmically expressed genes from 727 to 1,233—indicative of a clock re-gearing rather than clock disruption. Extending our analysis to exon-level quantification reveals that differential exon usage constitutes an independent regulatory layer, targeting processes not captured by transcript abundance alone, including SAM metabolism, ferroptosis and mRNA processing. Circadian rhythmicity in exon usage is demonstrated here for the first time. Sexual dimorphism is pervasive but primarily quantitative, reflecting differences in the magnitude and temporal precision of a conserved programme rather than divergent regulatory logic. This open-access, multi-layered dataset provides a comprehensive resource for the study of nutritional and circadian regulation of liver metabolism.

This dataset

Open GSE328655 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 GSE328655_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 PRJNA1456079 and SRA study SRP693597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

80 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 80 sample titles: 80 distinct titles with little repetition. 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

GSM9686717 liver, fasted, CT8, replicate 1, male
GSM9686718 liver, fasted, CT8, replicate 2, male
GSM9686719 liver, fasted, CT8, replicate 1, female
GSM9686720 liver, fasted, CT8, replicate 2, female
GSM9686721 liver, control, CT8, replicate 1, male
GSM9686722 liver, control, CT8, replicate 2, male
GSM9686723 liver, control, CT8, replicate 1, female
GSM9686724 liver, control, CT8, replicate 2, female
GSM9686725 liver, fasted, CT12, replicate 1, male
GSM9686726 liver, fasted, CT12, replicate 2, male
GSM9686727 liver, fasted, CT12, replicate 1, female
GSM9686728 liver, fasted, CT12, replicate 2, female
GSM9686729 liver, control, CT12, replicate 1, male
GSM9686730 liver, control, CT12, replicate 2, male
GSM9686731 liver, control, CT12, replicate 1, female
GSM9686732 liver, control, CT12, replicate 2, female
GSM9686733 liver, fasted, CT16, replicate 1, male
GSM9686734 liver, fasted, CT16, replicate 2, male
GSM9686735 liver, fasted, CT16, replicate 1, female
GSM9686736 liver, fasted, CT16, replicate 2, female
GSM9686737 liver, control, CT16, replicate 1, male
GSM9686738 liver, control, CT16, replicate 2, male
GSM9686739 liver, control, CT16, replicate 1, female
GSM9686740 liver, control, CT16, replicate 2, female
GSM9686741 liver, fasted, CT20, replicate 1, male
GSM9686742 liver, fasted, CT20, replicate 2, male
GSM9686743 liver, fasted, CT20, replicate 1, female
GSM9686744 liver, fasted, CT20, replicate 2, female
GSM9686745 liver, control, CT20, replicate 1, male
GSM9686746 liver, control, CT20, replicate 2, male
GSM9686747 liver, control, CT20, replicate 1, female
GSM9686748 liver, control, CT20, replicate 2, female
GSM9686749 liver, fasted, CT24, replicate 1, male
GSM9686750 liver, fasted, CT24, replicate 2, male
GSM9686751 liver, fasted, CT24, replicate 1, female
GSM9686752 liver, fasted, CT24, replicate 2, female
GSM9686753 liver, control, CT24, replicate 1, male
GSM9686754 liver, control, CT24, replicate 2, male
GSM9686755 liver, control, CT24, replicate 1, female
GSM9686756 liver, control, CT24, replicate 2, female

+ 40 more — browse all 80 samples with per-sample file links →

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Search all mouse RNA-seq datasets in GEO →

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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.