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Effects of mechanical stretch and depletion of lamin A/C on chromatin accessibility in human myotubes (ATACseq)

GSE288984 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2025/09/19 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
14 samples: 4 × human myotubes, siLaminsA/C, Hours72, static, vs 4 × human myotubes, siControl, Hours72, stretch, vs 3 × human myotubes, siControl, Hours72, static, vs 3 × human myotubes, siLaminsA/C, Hours72, stretch,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 GSE288984 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE288984_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1220159 and SRA study SRP562058. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41126185) ↗
Study design
4 × human myotubes, siLaminsA/C, Hours72, static, vs 4 × human myotubes, siControl, Hours72, stretch, vs 3 × human myotubes, siControl, Hours72, static, vs 3 × human myotubes, siLaminsA/C, Hours72, stretch,

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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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