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Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation [RNA-seq]

GSE309939 Mus musculus (mouse) RNA-seq (gene expression) 47 samples Submitted 2026/06/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 47 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
47 samples: 16 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.
Summary (written by the submitters)
Transcription factor (TF) expression and dosage regulate developmental cell fate decisions. Increased TF dosage has been predicted to enhance expression of high-affinity target genes but also increase the binding of lower-affinity loci. The relative importance of high- versus lower-affinity TF binding in guiding cell fate decisions remains unclear.
Read the full summary ↓
To test the roles of TF dosage, we examined the effects of increasing the dosage of MyoD1, the ?master regulator of myogenesis?, on skeletal muscle differentiation. Unexpectedly, increased MyoD1 dosage inhibited canonical myogenesis and redirected myoblast differentiation towards forming spontaneously contracting myotubes. This novel phenotype was driven by the MyoD1-dose-dependent upregulation of non-myogenic genes, including cell adhesion genes whose ectopic expression also inhibited classical myogenic differentiation and enabled myotube contraction. Live-cell single-molecule imaging showed that elevated MyoD1 dosage increased total chromatin binding and CUT&RUN profiling demonstrated that this increase occurred via preferential binding to lower-affinity loci. Integration of CUT&RUN, ATAC-seq and RNA-seq experiments revealed that increased MyoD1 binding correlated to the upregulation of otherwise unexpressed or lowly expressed genes. These findings suggest that increased MyoD1 dosage induced a selective gene regulatory expansion from high- to lower-affinity cis-regulatory elements, leading to activation of a broader ensemble of target genes, revealing a TF dose-dependent mechanism that can trigger distinct developmental programs. This submission contains additional RNA-seq samples generated that should be added to existing GEO Series GSE309864.
This dataset
Open GSE309939 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 GSE309939_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 PRJNA1364018 and SRA study SRP644556. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly in triplicate
C2C12 cells, iMyoD1, no differentiation, dox … ×3 C2C12 cells, iMyoD1, no differentiation, untr… ×3 C2C12 cells, iMyoD1, 24 h serum starvation, d… ×3 C2C12 cells, iMyoD1, 24 h serum starvation, u… ×3 C2C12 cells, iCdh23, 48 h serum starvation, u… ×3 C2C12 cells, iCdh23, 48 h serum starvation, d… ×3 C2C12 cells, iMcam, 48 h serum starvation, un… ×3 C2C12 cells, iMcam, 48 h serum starvation, do… ×3 +8 more

Supports a between-group comparison across 47 samples.

How we read this: 16 replicated groups read from 47 sample titles; they account for 47 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

+ 7 more — browse all 47 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.