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Mechanomemory of pulmonary fibroblasts demonstrates reversibility of transcriptomics and contraction phenotypes

GSE262420 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2024/12/31 Platform GPL23479

At a glance

RNA-seq (gene expression) · mouse · 20 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: 20 samples: 5 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: Mechanomemory of pulmonary fibroblasts demonstrates reversibility of transcriptomics and contraction phenotypesBiomaterials · 2025

Summary (written by the submitters)

Fibroblasts are cells responsible for producing extracellular matrix (ECM) components, which provides physical support for organs. Although these mesenchymal cells are responsive to mechanical cues in their environment, the permanence of these mechano-phenotypes is not well defined. We investigated the mechano-memory of lung fibroblasts and determined how switching culture conditions modulate cell responses and function.

Read the full summary ↓

Primary murine lung fibroblasts were isolated and cultured on 2D tissue culture plates or within 3D collagen hydrogels and were then passaged within the same or opposite culture condition to assess changes in gene expression, protein production, fibroblast subpopulation, contractile behavior, and traction forces. Compared to fibroblasts isolated on 2D tissue culture plates, fibroblasts within 3D hydrogels exhibited a decreased activation phenotype including reduced contraction profiles, diminished cell traction forces and decreased αSMA gene expression. Cells initially isolated via 2D culture and then cultured in 3D hydrogels exhibited a reversal in activation phenotype as measured by gene expression and contraction profiles. Bulk RNAseq identified groups of genes that exhibit reversible and non-reversable expression patterns. Overall, these findings indicate that lung fibroblasts have a mechanical memory that is altered by culture condition and can be reversible through precondition of cells within a softer 3D microenvironment.

Published in

Mechanomemory of pulmonary fibroblasts demonstrates reversibility of transcriptomics and contraction phenotypes

Novak CM, Wheat JS, Ghadiali SN et al. · Biomaterials 2025 · PMID 39276408 · doi:10.1016/j.biomaterials.2024.122830

This dataset

Open GSE262420 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 GSE262420_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 PRJNA1091687 and SRA study SRP497742. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39276408) ↗

Study design

5 conditions, mostly with about 4 replicates each

Lung, 2D-2D ×4 Lung, 2D-3D ×4 Lung, 3D-2D ×4 Lung, 3D-3D ×4 Lung, Sort_Fib ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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

GSM8169411 Lung, 2D-2D_1 Lung, 2D-2D
GSM8169412 Lung, 2D-2D_2 Lung, 2D-2D
GSM8169413 Lung, 2D-2D_3 Lung, 2D-2D
GSM8169414 Lung, 2D-2D_4 Lung, 2D-2D
GSM8169415 Lung, 2D-3D_1 Lung, 2D-3D
GSM8169416 Lung, 2D-3D_2 Lung, 2D-3D
GSM8169417 Lung, 2D-3D_3 Lung, 2D-3D
GSM8169418 Lung, 2D-3D_4 Lung, 2D-3D
GSM8169419 Lung, 3D-2D_1 Lung, 3D-2D
GSM8169420 Lung, 3D-2D_2 Lung, 3D-2D
GSM8169421 Lung, 3D-2D_3 Lung, 3D-2D
GSM8169422 Lung, 3D-2D_4 Lung, 3D-2D
GSM8169423 Lung, 3D-3D_1 Lung, 3D-3D
GSM8169424 Lung, 3D-3D_2 Lung, 3D-3D
GSM8169425 Lung, 3D-3D_3 Lung, 3D-3D
GSM8169426 Lung, 3D-3D_4 Lung, 3D-3D
GSM8169427 Lung, Sort_Fib_1 Lung, Sort_Fib
GSM8169428 Lung, Sort_Fib_2 Lung, Sort_Fib
GSM8169429 Lung, Sort_Fib_3 Lung, Sort_Fib
GSM8169430 Lung, Sort_Fib_4 Lung, Sort_Fib

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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.