GEO series
A cellular cross-species RNA-seq atlas captures the transcriptional dynamics of myogenesis
GSE324958
Homo sapiens; Mus musculus
Expression profiling by high throughput sequencing
24 samples
Submitted 2026/03/16
Platform GPL24676Platform GPL24247
Summary
Skeletal muscle formation and regeneration is a tightly regulated process involving extensive transcriptional reprogramming as proliferating myoblasts fuse into mature myotubes. However, a comparative comprehensive analysis of the transcriptional landscape of humans and mouse myogenesis is missing. Here, we present a high-quality RNA-sequencing dataset profiling this transition in both mouse (C2C12) and human (LHCN-M2) myogenic cells. Samples were collected from proliferating myoblasts, the early differentiation phase, and from mature myocytes using identical protocols, ensuring stringent comparability. This unified dataset captures the major transcriptional shifts occurring in myoblasts, marking the onset of differentiation. Quality metrics, including PCA, read distribution, and clustering, confirmed high internal consistency across samples and species. Comparative analyses revealed shared global features of myogenesis but also distinct regulatory trajectories. Human differentiation showed early upregulation followed by suppression of metabolic and stress-related pathways, while structural and ECM-associated programs remained persistently elevated. In contrast, mouse C2C12 cells displayed early inflammatory activation and later enrichment of metabolic and contractile pathways typical of mature myotubes. Ortholog-based integration demonstrated decreasing cross-species correlation over time, indicating progressive reinforcement of species-specific differentiation programs. We additionally compared this bulk RNA-seq with tissue-derived myotubes from single-cell muscle datasets to determine which transcriptional programs are conserved in the in vitro models or which emerge only in vivo. This analysis delineates the conserved and context-specific features of myogenesis, identifying pathways that reflect culture-specific artifacts in both human and mouse muscle cells.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE324958_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 24 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1438151 and SRA study SRP684092. Searching any of these in the dataset finder brings you back here.
Study design
6 conditions, mostly with about 4 replicates each
C2C12, day0 ×4
C2C12, day1 ×4
C2C12, day6 ×4
LHCNM2, day0 ×4
LHCNM2, day1 ×4
LHCNM2, day12 ×4
Supports a between-group comparison across 24 samples.
6 replicated groups read from 24 sample titles; they account for 24 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9589326 C2C12, day0-1
- GSM9589327 C2C12, day0-2
- GSM9589328 C2C12, day0-3
- GSM9589329 C2C12, day0-4
- GSM9589330 C2C12, day1-1
- GSM9589331 C2C12, day1-2
- GSM9589332 C2C12, day1-3
- GSM9589333 C2C12, day1-4
- GSM9589334 C2C12, day6-1
- GSM9589335 C2C12, day6-2
- GSM9589336 C2C12, day6-3
- GSM9589337 C2C12, day6-4
- GSM9589338 LHCNM2, day0-1
- GSM9589339 LHCNM2, day0-2
- GSM9589340 LHCNM2, day0-3
- GSM9589341 LHCNM2, day0-4
- GSM9589342 LHCNM2, day1-1
- GSM9589343 LHCNM2, day1-2
- GSM9589344 LHCNM2, day1-3
- GSM9589345 LHCNM2, day1-4
- GSM9589346 LHCNM2, day12-1
- GSM9589347 LHCNM2, day12-2
- GSM9589348 LHCNM2, day12-3
- GSM9589349 LHCNM2, day12-4
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