GEO series

Glucocorticoid-dependence and independence of the circadian liver transcriptome

GSE280339 Mus musculus (mouse) RNA-seq (gene expression) 52 samples Submitted 2026/01/09 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 52 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: 52 samples: 51 distinct titles, 1 of them repeatedGroups 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: Glucocorticoid-dependence and independence of the circadian liver transcriptomeNpj biological timing and sleep · 2026

Summary (written by the submitters)

The liver, a critical metabolic organ, shows clear day-night variation in patterns of gene and protein expression, and in metabolic pathway activity. Liver cells possess molecular circadian clocks, but systemic factors also contribute to the circadian rhythmicity of liver gene expression. Here, we examine the role of glucocorticoid signalling.

Read the full summary ↓

Glucocorticoids are essential hormones, with a strong circadian oscillation, which control multiple cellular processes via their action on the glucocorticoid receptor (GR). We first compare clock factor and GR binding at promoters and enhancers linked to rhythmic genes, and find increased clock factor binding at those elements where GR is also present. We find that genes with GR binding at the promoter are more likely to show rhythmic expression. We go to test the role of GR more directly, by examining circadian rhythms of gene expression in mice with and without hepatocyte-targeted GR deletion. Notably, we observe only a small effect of GR deletion, with the vast majority of rhythmic genes showing unchanged rhythmic expression, despite evidence for GR binding in the vicinity of these genes. We do find a small number of genes to show lost or gained rhythmicity with GR deletion, and genes which lose rhythmicity do associate with GR binding sites. However, GR appears redundant for conveying timing information to most of the rhythmic liver transcriptome, a conclusion which is supported by our re-analysis of an independent published dataset.

Published in

Glucocorticoid-dependence and independence of the circadian liver transcriptome

Maidstone RJ, Hunter AL, Iqbal M et al. · Npj biological timing and sleep 2026 · PMID 41641009 · doi:10.1038/s44323-025-00068-8

This dataset

Open GSE280339 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 GSE280339_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 PRJNA1177879 and SRA study SRP540886. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41641009) ↗

Study design

51 distinct titles, 1 of them repeated

HET 48 M ×2

How we read this: Read from 52 sample titles: 51 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

GSM8594762 WT 0 M
GSM8594763 HET 0 F
GSM8594764 WT 2 F
GSM8594765 HET 2 F
GSM8594766 WT 4 M
GSM8594767 HET 4 M
GSM8594768 WT 6 F
GSM8594769 HET 6 F
GSM8594770 WT 8 M
GSM8594771 HET 8 M
GSM8594772 WT 10 F
GSM8594773 HET 10 F
GSM8594774 WT 12 M
GSM8594775 HET 12 M
GSM8594776 WT 14 F
GSM8594777 HET 14 F
GSM8594778 WT 16 M
GSM8594779 HET 16 M
GSM8594780 WT 18 F
GSM8594781 HET 18 F
GSM8594782 WT 20 M
GSM8594783 HET 20 M
GSM8594784 WT 22 F
GSM8594785 HET 22 F
GSM8594786 WT 24 M
GSM8594787 HET 24 M
GSM8594788 WT 26 F
GSM8594789 HET 26 F
GSM8594790 WT 28 M
GSM8594791 HET 28 M
GSM8594792 WT 30 F
GSM8594793 HET 30 F
GSM8594794 WT 32 M
GSM8594795 HET 32 M
GSM8594796 WT 34 F
GSM8594797 HET 34 F
GSM8594798 WT 36 M
GSM8594799 HET 36 M
GSM8594800 WT 38 F
GSM8594801 HET 38 F

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

GSE267727 Transcriptome profiling of non-islet metabolic tissues in ~500 DO mouse liver, adipose, heart, and skeletal muscle tissue from mice fed high-fat, high-sugar diet [heart] 482 samples shares liver
GSE282210 Transcriptome analysis of quiescent livers and regenerating livers after partial hepatectomy (PH) in young and aged mice 133 samples shares liver
GSE252621 Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice 62 samples shares liver
GSE301899 mTOR signaling contributes to system-driven rhythmic gene expression in mouse liver 282 samples shares liver
GSE297702 Light and sex modify Snord116 genotype effects on metabolism, behavior, and imprinted gene networks following circadian entrainment 219 samples shares circadian
GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares liver
GSE269328 Glucagon receptor agonism and treatment withdrawal effect on liver transcriptomes of diet-induced obese mice 24 samples shares liver
GSE244388 PCB126 Modifies the Murine Hepatic Transcriptome and Metallome to Promote Alcohol-associated Liver Disease Pathogenesis 24 samples shares liver

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.