GEO series

Transcriptomic Profile of Skeletal Muscle Biopsies from Duchenne and Becker Muscular Dystrophy Patients

GSE291383 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/07/30 Platform GPL21697

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 12 × skeletal muscle, dmd, d vs 6 × skeletal muscle, bmd, bGroups 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)

The complexity of RNA metabolism has become crucial in neuromuscular diseases, especially for Duchenne Muscular Dystrophy (DMD) and Becker Muscular Dystrophy (BMD). DMD is associated with mutations in Dystrophin gene that disrupt the protein reading frame causing premature stop codons. In contrast, patients with BMD usually have in-frame deletions that maintain the correct reading frame.

Read the full summary ↓

Our goal is to search for possible pathways that differs between the two diseases, in which DMD develop a severe phenotype compared to BMD. Here we aimed to evaluate the transcriptomic profile in muscle biopsy of DMD and BMD patients. We collected RNA obtained from muscle biopsy of pediatric DMD patients (n=12) and BMD patients (n=6). Through RNA sequencing, the differentially expressed (DE) genes of DMD patients versus BMD patients were analyzed. Through principal component analysis (PCA), we were able to identify a clear difference between the two groups based on gene expression pattern. DMD patients compared to BMD patients showed a particular activation of genes involved in collagen synthesis, extracellular matrix organization, and oncostatin M-dependent pathways, which plays an important role in the fibrosis process. This suggests that a more severe phenotype in DMD than BMD patients may be due to greater deregulation of these pathways, reflecting the clinical picture of patients observed. Furthermore mRNAs expression levels evaluated by RT-qPCR confirmed RNA-seq data. Enrichment pathways analysis revealed the strong alteration in collagen synthesis and extracellular matrix organization, suggesting different severity degree in the establishment of fibrotic processes. All the collagen genes validated by RT-qPCR were strongly upregulated in DMD patients. This study provides preliminary insights into the difference in gene expression between the two groups and lays the basis for the identification of possible mechanism that differentiate between the two diseases.

This dataset

Open GSE291383 in finder → Find more human 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 GSE291383_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 PRJNA1233273 and SRA study SRP568689. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 × skeletal muscle, dmd, d vs 6 × skeletal muscle, bmd, b

Supports a between-group comparison across 18 samples.

How we read this: 2 replicated groups read from 18 sample titles; they account for 18 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

GSM8834096 skeletal muscle, bmd, b1 skeletal muscle, bmd, b
GSM8834097 skeletal muscle, bmd, b2 skeletal muscle, bmd, b
GSM8834098 skeletal muscle, bmd, b3 skeletal muscle, bmd, b
GSM8834099 skeletal muscle, bmd, b4 skeletal muscle, bmd, b
GSM8834100 skeletal muscle, bmd, b5 skeletal muscle, bmd, b
GSM8834101 skeletal muscle, bmd, b6 skeletal muscle, bmd, b
GSM8834102 skeletal muscle, dmd, d1 skeletal muscle, dmd, d
GSM8834103 skeletal muscle, dmd, d2 skeletal muscle, dmd, d
GSM8834104 skeletal muscle, dmd, d3 skeletal muscle, dmd, d
GSM8834105 skeletal muscle, dmd, d4 skeletal muscle, dmd, d
GSM8834106 skeletal muscle, dmd, d5 skeletal muscle, dmd, d
GSM8834107 skeletal muscle, dmd, d6 skeletal muscle, dmd, d
GSM8834108 skeletal muscle, dmd, d7 skeletal muscle, dmd, d
GSM8834109 skeletal muscle, dmd, d8 skeletal muscle, dmd, d
GSM8834110 skeletal muscle, dmd, d9 skeletal muscle, dmd, d
GSM8834111 skeletal muscle, dmd, d10 skeletal muscle, dmd, d
GSM8834112 skeletal muscle, dmd, d11 skeletal muscle, dmd, d
GSM8834113 skeletal muscle, dmd, d12 skeletal muscle, dmd, d

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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.