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Decreased chondrocyte features of articular cartilage during short-term repeated overloading: a synovium-cartilage interaction via inhibin subunit beta A

GSE280656 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2025/03/05 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 10 conditions, mostly in triplicateGroups 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
Short-term overloading exercise attenuates articular chondrocyte features partly via synovium-cartilage interactions mediated by inhibin subunit beta AScientific reports · 2025
Summary (written by the submitters)
The primary goal of this study is to investigate the ultrashort-term responses and molecular mechanisms in both the synovium and cartilage under conditions of excessive mechanical loading, a major contributing factor in the pathogenesis of osteoarthritis (OA). While cartilage degeneration is a hallmark of OA, the involvement of the synovium in disease progression and pain, particularly in relation to synovitis, has been increasingly recognized.
Read the full summary ↓
Despite this, the immediate molecular changes in both tissues following mechanical stress, and the interactions between them, remain unclear. To address these gaps, we developed a mouse model that simulates excessive mechanical loading through treadmill exercise combined with weight attachment. We investigated the ultrashort-term gene expression changes in the synovium and cartilage at 1, 4, and 24 hours post-exercise using RNA sequencing (RNA-seq). Additionally, we examined the effects of repeated overloading by analyzing tissue samples from mice subjected to four consecutive days of overloading. This approach allowed us to capture both the acute and repeated stress responses in these tissues. Through transcriptomic analysis, we aimed to identify key molecular mediators driving both the rapid transcriptional changes in each tissue and the synovium-cartilage interaction.
Published in
Short-term overloading exercise attenuates articular chondrocyte features partly via synovium-cartilage interactions mediated by inhibin subunit beta A
Arino Y, Terashima A, Tsubaki T et al. · Scientific reports 2025 · PMID 40000838 · doi:10.1038/s41598-025-91742-1
This dataset
Open GSE280656 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 GSE280656_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 PRJNA1179905 and SRA study SRP542068. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40000838) ↗
Study design
10 conditions, mostly in triplicate
Syn_Control ×3 Syn_Single_1hr ×3 Syn_Single_4hr ×3 Syn_Single_24hr ×3 Syn_Repeated_24hr ×3 Cart_Control ×3 Cart_Single_1hr ×2 Cart_Single_4hr ×2 +2 more

Supports a between-group comparison across 26 samples.

How we read this: 10 replicated groups read from 26 sample titles; they account for 26 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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