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Comparative transcriptomic studies to determine the molecular effects of titin mechanical knock-out in skeletal muscles

GSE271916 Mus musculus (mouse) RNA-seq (gene expression) 56 samples Submitted 2025/03/27 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 56 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
Mus musculus (mouse)
Samples
56 samples: 14 conditions, mostly with about 4 replicates eachGroups 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
Mechanically knocking out titin reveals protein tension loss as a trigger of muscle diseaseNature biomedical engineering · 2025
Summary (written by the submitters)
Mechanical knock-out (mKO) is a novel tool to study the role of mechanical proteins in physiology by ceasing their force transmission in vivo. Here, titin protein carriying TEV protease recognition site (TEVs-TTN) is cleaved in vivo by the AAV-driven overexpression of TEV protease (TEVp) in skeletal muscles. An acute form of myopathy appears encompassing myofiber atrophy, myonuclei internalization, mitochondrial mislocalization and aggregation, and intersticial fibrosis.
Read the full summary ↓
To define the molecular pathways affected when titin mechanics are perturbed, we performed RNA-sequencing with WT and homozygous Tttin mKO at 3 different timempoints and heterozygous Titin mKO muscles including saline-injected (-TEVp) and AAV-injected legs (+TEVp).
Published in
Mechanically knocking out titin reveals protein tension loss as a trigger of muscle disease
Silva-Rojas R, Vicente N, Gavilán-Herrera M et al. · Nature biomedical engineering 2025 · PMID 40473933 · doi:10.1038/s41551-025-01403-x
This dataset
Open GSE271916 in finder → Find more mouse 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 GSE271916_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 PRJNA1134116 and SRA study SRP519087. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40473933) ↗
Study design
14 conditions, mostly with about 4 replicates each
WT muscle, AAV, 3 dpi, sample ×5 HOMO mKo muscle, AAV, 7 dpi, sample ×5 HOMO mKO muscle, NaCl, 3 dpi, sample ×4 HOMO mKO muscle, AAV, 3 dpi, sample ×4 WT muscle, AAV, 7 dpi, sample ×4 HOMO mKo muscle, NaCl, 7 dpi, sample ×4 HET mKo muscle, NaCl, 7 dpi, sample ×4 HET mKo muscle, AAV, 7 dpi, sample ×4 +6 more

Supports a between-group comparison across 56 samples.

How we read this: 14 replicated groups read from 56 sample titles; they account for 56 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.