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Differentiation and Dexamethasone Atrophy on C2C12 myotubes

GSE300503 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/09/29 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 6 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
Early regulation and alternative splicing dynamics in glucocorticoid muscle atrophy revealed by temporal omics in C2C12 myotubesAmerican journal of physiology. Cell physiology · 2025
Summary (written by the submitters)
Skeletal muscle atrophy and weakness are major contributors to morbidity, prolonged recovery, and long-term disability across a wide range of diseases. Atrophy is caused by breakdown of sarcomeric proteins resulting in loss of muscle mass and strength. Molecular mechanism underlying the onset of muscle atrophy and its progression have been analysed in patients, mice, and cell culture but the complementarity of these model systems remains to be explored.
Read the full summary ↓
Here, we applied deep-coverage transcriptomic and proteomic profiling to characterize dynamic changes during dexamethasone-induced atrophy in the widely used murine skeletal muscle cell line C2C12. Comparison with published datasets confirmed that muscle differentiation is well recapitulated in C2C12 myotubes. Under dexamethasone-induced treatment, this model was particularly suited to capture early atrophy events, prior to disassembly and degradation of sarcomeric proteins. We also identified alterations in mitochondrial gene expression and differential alternative splicing events during early-stage myotube atrophy. This dataset complements existing in vivo data and provides novel insights into the regulatory processes during skeletal muscle wasting.
Published in
Early regulation and alternative splicing dynamics in glucocorticoid muscle atrophy revealed by temporal omics in C2C12 myotubes
Nakagawa S, Misios A, Popp O et al. · American journal of physiology. Cell physiology 2025 · PMID 40920643 · doi:10.1152/ajpcell.00518.2025
This dataset
Open GSE300503 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 GSE300503_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 PRJNA1281074 and SRA study SRP594069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40920643) ↗
Study design
6 conditions, mostly with about 4 replicates each
C2C12 cells, Day 0 myoblasts ×4 C2C12 cells, Day 7 myotubes ×4 C2C12 cells, Day 8, atrophied myotubes ×4 C2C12 cells, Day 8, control-treated myotubes ×4 C2C12 cells, Day 10, atrophied myotubes ×4 C2C12 cells, Day 10, control-treated myotubes ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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
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