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Sphingolipids in extracellular vesicles released from the skeletal muscle plasma membrane control muscle stem cell fate during muscle regeneration

GSE294455 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/11/13 Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 10 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
10 samples: 5 × Human skeletal muscle cells from healthy subject# vs 5 × TNFalpha treated Human skeletal muscle cells from healthy subject#Groups 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
Sphingolipids in Extracellular Vesicles Released From the Skeletal Muscle Plasma Membrane Control Muscle Stem Cell Fate During Muscle RegenerationJournal of extracellular vesicles · 2025
Summary (written by the submitters)
Extracellular vesicles (EVs) represents a cytokine-independent pathway by which skeletal muscle (SkM) cells modulate the fate of neighbouring cells to control SkM homeostasis. Here we show that SkM release a bulk of small (sEVs) and large (lEVs), both generated from plasma membrane (PM). Conversely to lEVs, sEVs are synthesized from membrane folds enriched in Alix and TSG101 proteins and lipid-rafts, which have never been described for other cell types.
Read the full summary ↓
During muscle regeneration, sEVs promoted M1 macrophage polarization and migration and MuSC differentiation, contributing to accelerated muscle regeneration, whereas lEVs influenced the shift from a pro-inflammatory to an anti-inflammatory response, promoting MuSC proliferation. The lipid composition of sEVs and lEVs, particularly the ratios of sphingosine 1-phosphate (d18:1 and d16:1), explained their differential effects, with TNF-α altering these ratios and modifying SkM-EV actions. Our work highlight the role of sub-populations of SkM-EVs in muscle regeneration, and their potential for therapeutic applications.
Published in
Sphingolipids in Extracellular Vesicles Released From the Skeletal Muscle Plasma Membrane Control Muscle Stem Cell Fate During Muscle Regeneration
Hakkar R, Brun CE, Leblanc P et al. · Journal of extracellular vesicles 2025 · PMID 40984725 · doi:10.1002/jev2.70164
This dataset
Open GSE294455 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 GSE294455_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 PRJNA1249486 and SRA study SRP577794. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40984725) ↗
Study design
5 × Human skeletal muscle cells from healthy subject# vs 5 × TNFalpha treated Human skeletal muscle cells from healthy subject#

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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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