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The Core Circadian Clock Factor, Bmal1, Transduces Sex-specific Differences in Both Rhythmic and Nonrhythmic Gene Expression in the Mouse Heart

GSE262714 Mus musculus (mouse) RNA-seq (gene expression) 96 samples Submitted 2024/12/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 96 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
96 samples: 48 conditions, mostly in duplicateGroups 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 Core Circadian Clock Factor, Bmal1, Transduces Sex-specific Differences in Both Rhythmic and Nonrhythmic Gene Expression in the Mouse HeartFunction (Oxford, England) · 2025
Summary (written by the submitters)
Sexual dimorphism in mammals, including humans and laboratory rodents, has primarily been attributed to hormonal and sex chromosomal differences. Accumulating evidence now suggests that circadian rhythms also contribute to sexual dimorphism in cardiac physiology and cardiovascular diseases. Here, we show that the circadian transcriptome of the mouse heart exhibits sexual dimorphism.
Read the full summary ↓
We determined that female hearts express significantly more rhythmically expressed genes (REGs) and that the temporal distribution of the REGs was different between males and females. In addition, the overlap in genes and functional pathways were modest between males and females. All aspects of the sexual dimorphism in the circadian transcriptome was significantly diminished with cardiomyocyte specific loss of the core clock gene, Bmal1. Analysis of all differentially expressed genes (DEGs) between males and females showed that differential expression between sexes was largely diminished with loss of cardiomyocyte Bmal1. We conclude that cardiomyocyte specific Bmal1, and likely the core clock mechanism, plays a vital role in conferring a sexually dimorphic program of gene expression in the adult mouse heart.
Published in
The Core Circadian Clock Factor, Bmal1, Transduces Sex-specific Differences in Both Rhythmic and Nonrhythmic Gene Expression in the Mouse Heart
Zhang X, Procopio SB, Ding H et al. · Function (Oxford, England) 2025 · PMID 39658371 · doi:10.1093/function/zqae053
This dataset
Open GSE262714 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 GSE262714_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 PRJNA1093049 and SRA study SRP498547. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39658371) ↗
Study design
48 conditions, mostly in duplicate
Tam_F_ct18 ×2 Tam_F_ct22 ×2 Tam_F_ct26 ×2 Tam_F_ct30 ×2 Tam_F_ct34 ×2 Tam_F_ct38 ×2 Tam_F_ct42 ×2 Tam_F_ct46 ×2 +40 more

Supports a between-group comparison across 96 samples.

How we read this: 48 replicated groups read from 96 sample titles; they account for 96 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

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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