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Control of Circadian Glucose Metabolism through BMAL1-HIF Axis in Obesity

GSE282908 Mus musculus (mouse) RNA-seq (gene expression) 51 samples Submitted 2025/04/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 51 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
51 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
Control of circadian muscle glucose metabolism through the BMAL1-HIF axis in obesityProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
Disruptions of circadian rhythms is widespread in modern society and leads to accelerated and worsened symptoms of metabolic syndrome. In healthy mice, the circadian clock factor BMAL1 is required for skeletal muscle function and metabolism. However, the importance of muscle BMAL1 in the development of metabolic diseases, such as diet-induced obesity (DIO), remains unclear.
Read the full summary ↓
Here, we demonstrate that skeletal muscle-specific BMAL1-deficient mice exhibit worsened glucose tolerance upon high fat diet feeding, despite no evidence of increased weight gain. Metabolite profiling from Bmal1-deficient muscles revealed impaired glucose utilization specifically at early steps in glycolysis that dictate the switch between anabolic and catabolic glucose fate. We provide evidence that this is due to abnormal control of the nutrient stress-responsive hypoxia inducible factor (HIF) pathway. Genetic HIF1α stabilization in muscle Bmal1-deficient mice restores glucose tolerance and expression of approximately 30% of dysregulated genes during DIO, including glycolytic enzymes. Together, these data indicate that during DIO, skeletal muscle BMAL1 is an important regulator of HIF-driven glycolysis and metabolic flexibility, which influences the development of high fat diet-induced glucose intolerance.
Published in
Control of circadian muscle glucose metabolism through the BMAL1-HIF axis in obesity
Chaikin CA, Thakkar AV, Steffeck AWT et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40127275 · doi:10.1073/pnas.2424046122
This dataset
Open GSE282908 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 GSE282908_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 PRJNA1190984 and SRA study SRP547759. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40127275) ↗
Study design
8 conditions, mostly with about 4 replicates each
Muscle, HFD, Control (Bmal1/fx/fx), Animal ×15 Muscle, HFD, Bmal1KO, Animal ×9 Muscle, HFD, Control (Bmal1fx/fx;Vhlfx/fx), A… ×6 Muscle, HFD, Control (Vhlfx/fx), Animal ×6 Muscle, RC, Control (Bmal1/fx/fx), Animal ×4 Muscle, HFD, Bmal1KO;VhlKO, Animal ×4 Muscle, HFD, VhlKO, Animal ×4 Muscle, RC, Bmal1KO, Animal ×3

Supports a between-group comparison across 51 samples.

How we read this: 8 replicated groups read from 51 sample titles; they account for 51 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

+ 11 more — browse all 51 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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