GEO series

Identification of novel mRNA splicing isoforms in human myogenesis

GSE287954 Homo sapiens (human) RNA-seq (gene expression) 72 samples Submitted 2025/11/18 Platform GPL24676Platform GPL28975

At a glance

RNA-seq (gene expression) · human · 72 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: 72 samples
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: In-vitro human myogenesis model reveals novel mRNA alternative splicing isoformsScientific reports · 2025

Summary (written by the submitters)

Myogenesis, the process of muscle formation and regeneration, requires significant changes in gene expression program. However, alternative splicing during human myogenesis has not been systematically studied. Here, we examined mRNA splicing changes during myogenesis in two human myoblast cell lines using hybrid transcriptomic approaches by combining short-read (Illumina) and long-read (Nanopore) RNA-seq analyses.

Read the full summary ↓

We identified 13,853 new significant splicing isoforms (60,582 in total), with RNAs increasing and decreasing in abundance between days 0 and 3 (3,771 and 3,649, respectively), and between days 3 and 5 (1,302 and 1,109, respectively). We identified 1,937 significant differential transcript usage events (DTU), which pathways were involved in muscle regulation. Findings were validated using RT-qPCR and across mouse and human models, including clinical samples from peripheral artery disease patients. Artificial Intelligence algorithms predicted 595 myogenesis-associated high-confidence novel protein-coding splicing isoforms. Our findings underscore the importance of mRNA splicing isoforms in muscle biology.

Published in

In-vitro human myogenesis model reveals novel mRNA alternative splicing isoforms

Donega S, Banskota N, Yang JH et al. · Scientific reports 2025 · PMID 41034476 · doi:10.1038/s41598-025-16523-2

This dataset

Open GSE287954 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 GSE287954_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 PRJNA1215354 and SRA study SRP559780. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41034476) ↗

Samples in this study

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+ 72 more — browse all 72 samples with per-sample file links →

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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.