GEO series

siPiezo1 or scRNA immortalised MSC cell line (Y201) cultured on stiff hydrogels

GSE288423 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/08/20 Platform GPL30173

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × Stiff V- scRNA vs 3 × Stiff V- siPiezo vs 3 × Stiff V+ scRNA vs 3 × Stiff V+ siPiezo1Groups 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: Piezo1 regulates the mechanotransduction of soft matrix viscoelasticityNature communications · 2025

Summary (written by the submitters)

Mechanosensitive ion channels have emerged as fundamental proteins in sensing extracellular matrix (ECM) mechanics. Among those, Piezo1 has been proposed as a key mechanosensor in cells. However, whether and how Piezo1 senses time-dependent ECM mechanical properties (i.e., viscoelasticity) remains unknown. To address this question, we combined an immortalised mesenchymal stem cell (MSC) line with adjustable Piezo1 expression with soft (400 Pa) and stiff (25 kPa) viscoelastic hydrogels with independently tuneable Young’s modulus and stress relaxation.

Read the full summary ↓

Here, we propose that Piezo1 is an important sensor of stiffness at this range (25kPa) consistent with the molecular clutch model. By performing RNA sequencing (RNA-seq), we identified the transcriptomic phenotype of MSCs response to matrix viscoelasticity and Piezo1 activity, highlighting gene signatures that drive MSCs mechanobiology at this elasticity scale.

Published in

Piezo1 regulates the mechanotransduction of soft matrix viscoelasticity

A G Oliva M, Ciccone G, Fläschner G et al. · Nature communications 2025 · PMID 41093846 · doi:10.1038/s41467-025-64185-5

This dataset

Open GSE288423 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 GSE288423_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1217413 and SRA study SRP560762. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41093846) ↗

Study design

3 × Stiff V- scRNA vs 3 × Stiff V- siPiezo vs 3 × Stiff V+ scRNA vs 3 × Stiff V+ siPiezo1

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8767475 Stiff V- scRNA1 Stiff V- scRNA
GSM8767476 Stiff V- scRNA2 Stiff V- scRNA
GSM8767477 Stiff V- scRNA3 Stiff V- scRNA
GSM8767478 Stiff V- siPiezo_1 Stiff V- siPiezo
GSM8767479 Stiff V- siPiezo_2 Stiff V- siPiezo
GSM8767480 Stiff V- siPiezo_3 Stiff V- siPiezo
GSM8767481 Stiff V+ scRNA1 Stiff V+ scRNA
GSM8767482 Stiff V+ scRNA2 Stiff V+ scRNA
GSM8767483 Stiff V+ scRNA3 Stiff V+ scRNA
GSM8767484 Stiff V+ siPiezo1_1 Stiff V+ siPiezo1
GSM8767485 Stiff V+ siPiezo1_2 Stiff V+ siPiezo1
GSM8767486 Stiff V+ siPiezo1_3 Stiff V+ siPiezo1

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