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Multiomics Analyses of Steroid Drug Efficacy in Duchenne Muscular Dystrophy Cardiomyocytes

GSE312779 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2026/05/05 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 48 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
Homo sapiens (human)
Samples
48 samples: 10 conditions, mostly with about 5 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.
Summary (written by the submitters)
Duchenne muscular dystrophy (DMD) is an X-linked degenerative disorder that causes progressive damage to skeletal and cardiac muscles, ultimately leading to premature mortality. The recently approved drug vamorolone (Agamree) demonstrates comparable efficacy in motor function improvement to conventional glucocorticoids, such as prednisolone, but with markedly reduced side effects.
Read the full summary ↓
Unlike many corticosteroids that increase blood volume and pressure, vamorolone exhibits cardioprotective properties. However, molecular characterization of these effects has been challenging because traditional DMD models, including the mdx mouse, fail to manifest the cardiac disease phenotypes observed in patients. Here, we established a representative dystrophic cardiomyopathy model by differentiating DMD patient-derived induced pluripotent stem cells into cardiomyocytes (DMD-CMs). Compared with healthy control CMs, DMD-CMs exhibited downregulated transcriptional signatures resulting in extracellular matrix stability, cardiac action potential regulation and cytoskeletal integrity. Using this disease model, we further assessed vamorolone treatment compared to other corticosteroids (prednisone, eplerenone, and aldosterone) using RNA-sequencing and high-resolution mass spectrometry-based metabolomics. All drug treatments altered the abundance of metabolites in the methionine cycle and downstream pathways in DMD-CMs. Vamorolone reprogrammed the transcriptional profiles associated with mitochondrial function, redox homeostasis, ER stress response, and actin binding when compared to prednisolone-treated DMD-CMs. Our gene-metabolite network analyses reveal that prednisolone significantly enhanced inflammatory processes and metabolically rewired the TCA flux shifting toward anaerobic glycolysis. Taken together, this represents the first integrated transcriptomic and metabolic analysis delineating the DMD cardiac
This dataset
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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 GSE312779_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 PRJNA1375868 and SRA study SRP651878. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly with about 5 replicates each
DMD Cardiomyocytes, DMSO, ×5 DMD Cardiomyocytes, Aldosterone, ×5 DMD Cardiomyocytes, Prednisolone, ×5 DMD Cardiomyocytes, Vamorolone, ×5 WT Cardiomyocytes, Prednisolone, ×5 WT Cardiomyocytes, Vamorolone, ×5 DMD Cardiomyocytes, Eplerenone, ×4 WT Cardiomyocytes, DMSO, ×4 +5 more

Supports a between-group comparison across 45 samples.

How we read this: 10 replicated groups read from 48 sample titles; they account for 45 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human 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.