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Transcriptomic analysis of Cr(VI)-induced changes in C2C12 cells during myogenic differentiation

GSE294800 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/09/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 10 conditions, mostly in triplicateGroups 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
Transcriptomic analysis of Cr(VI)-induced changes in C2C12 cells during myogenic differentiationJournal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS) · 2025
Summary (written by the submitters)
Hexavalent chromium [Cr(VI)] is an environmental toxicant extensively used in a variety of industrial processes including chrome plating, leather tanning, textile manufacturing, aircraft production, and stainless-steel production. Our previous study showed that exposure to Cr(VI) impaired C2C12 myogenic differentiation in a dose-dependent manner, yet the transcriptional mechanisms underlying Cr(VI)-induced disruption of myogenesis remains poorly understood.
Read the full summary ↓
Here, we performed bulk RNA-sequencing on C2C12 myoblasts undergoing differentiation in the presence of 0, 2, or 5 µM of Cr(VI). Differential gene expression analysis demonstrated a dose- and time-dependent increase in transcriptional dysregulation. Fuzzy c-means clustering identified 12 distinct gene expression patterns, with Clusters 3, 10, and 12 showing significant overlap with Cr(VI)-regulated genes. Functional enrichment analyses revealed Cr(VI) disrupts genes involved in early-stage cell cycle regulation and DNA repair as well as terminal differentiation processes like sarcomere organization and muscle contraction. Specifically, Cr(VI) impaired expression of key structural and contractile genes and disrupted DNA repair and cell cycle regulatory pathways, including downregulation of p21 and upregulation of proliferative marker PCNA. Furthermore, we identified suppression of Hippo signaling through downregulation of Tead4 and its muscle-specific downstream targets, providing a mechanism for impaired differentiation. These findings highlight widespread alterations in transcriptional programs governing muscle development and maturation, offering insight into how Cr(VI) exposure affects skeletal muscle health.
Published in
Transcriptomic analysis of Cr(VI)-induced changes in C2C12 cells during myogenic differentiation
Park SY, Sun H · Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS) 2025 · PMID 40803287 · doi:10.1016/j.jtemb.2025.127714
This dataset
Open GSE294800 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 GSE294800_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 PRJNA1251621 and SRA study SRP579075. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40803287) ↗
Study design
10 conditions, mostly in triplicate
C2C12 cells, Cr0, D0, biol ×3 C2C12 cells, Cr0, D1, biol ×3 C2C12 cells, Cr0, D2, biol ×3 C2C12 cells, Cr0, D4, biol ×3 C2C12 cells, Cr2, D1, biol ×3 C2C12 cells, Cr2, D2, biol ×3 C2C12 cells, Cr2, D4, biol ×3 C2C12 cells, Cr5, D1, biol ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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
Datasets on a similar topic

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