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Effects of mechanical stretch and depletion of lamin A/C on gene expression in human myotubes (RNAseq)

GSE289091 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/09/19 Platform GPL24676Platform 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: 7 × myotubes, siLaminsA/C, Hours72, static, vs 4 × myotubes, siControl, Hours72, stretch, vs 4 × myotubes, siLaminsA/C, Hours72, stretch, vs 2 × myotubes, siControl, Hours72, static,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
Lamin A/C protects chromatin accessibility during mechanical loading in human skeletal muscleCell communication and signaling : CCS · 2025
Summary (written by the submitters)
To investigate the effects of A-type lamins on chromatin accessibility during mechanical loading in human skeletal muscle, we established 72h differentiated muscle cells in which each target gene has been knocked down by siRNA.
Published in
Lamin A/C protects chromatin accessibility during mechanical loading in human skeletal muscle
Jabre S, Cherchame E, Pinzón N et al. · Cell communication and signaling : CCS 2025 · PMID 41126185 · doi:10.1186/s12964-025-02437-z
This dataset
Open GSE289091 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 GSE289091_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 PRJNA1221527 and SRA study SRP562693. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41126185) ↗
Study design
7 × myotubes, siLaminsA/C, Hours72, static, vs 4 × myotubes, siControl, Hours72, stretch, vs 4 × myotubes, siLaminsA/C, Hours72, stretch, vs 2 × myotubes, siControl, Hours72, static,

Supports a between-group comparison across 17 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 17 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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