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Acoustic modulation of mechanosensitive genes and adipocyte differentiation

GSE247726 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/03/12 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 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
Acoustic modulation of mechanosensitive genes and adipocyte differentiationCommunications biology · 2025
Summary (written by the submitters)
Eukaryotic cells are equipped with multiple mechanosensing systems and perceive wide range of mechanical stimuli from the environment. However, cell-level responses against acoustic waves, which transmits feeble but highly frequent physical perturbation, largely remains uninvestigated, especially with regard to audible range of sound.
Read the full summary ↓
Here we investigate the effect of acoustic stimulation on gene expression profiles of mammalian cultured cells. A direct sound emission system was set up using a vibrational transducer to directly generate acoustic waves in culture medium. A custom-made vibrating plate made of PEEK (poly ether ether ketone) plastic was used as a diaphragm. A set of sound patterns including single-frequency sound and white noise were generated by NCH Tone Generator software. Sound intensity was directly measured by recording it in water using a hydrophone and the pressure level was calculated. C2C12 myoblasts cultured in a plastic dish with approximately 50% confluency were subjected to acoustic stimulation. 440 Hz and 14k Hz single-frequency sine wave sound were selected as representatives of low and high audible frequencies, and white noise was selected as a random noise pattern. 2 and 24 hours after continuous emission of these sound at 100 Pa, total RNA was extracted and subjected to the gene expression profiling analysis by RNA-sequencing technique. Total 42 early- and 145 late-response genes were identified as sound-sensitive genes in 2 and 24 hours stimulation, respectively. Gene annotation analyses revealed that in addition to the known mechanosensitive activities such as fluid shear stress response, cell migration, cell adhesion and blood vessel development, variety of pathways and processes were identified to be affected by acoustic stimulation.
Published in
Acoustic modulation of mechanosensitive genes and adipocyte differentiation
Kumeta M, Otani M, Toyoda M et al. · Communications biology 2025 · PMID 40240542 · doi:10.1038/s42003-025-07969-1
This dataset
Open GSE247726 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 GSE247726_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 PRJNA1040218 and SRA study SRP471841. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40240542) ↗
Study design
8 conditions, mostly in triplicate
C2C12 cells, 440Hz, 2h, biol ×3 C2C12 cells, 14k, 2h, biol ×3 C2C12 cells, WN, 2h, biol ×3 C2C12 cells, silent, 2h, biol ×3 C2C12 cells, 440Hz, 24h, biol ×3 C2C12 cells, 14k, 24h, biol ×3 C2C12 cells, WN, 24h, biol ×3 C2C12 cells, silent, 24h, biol ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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