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Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs [ATAC-seq]

GSE292900 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2025/10/22 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
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
Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programsPLoS genetics · 2025
Summary (written by the submitters)
Dysregulation of the cellular mechanisms that coordinate the interpretation and transduction of microenvironmental biophysical signals are a unifying feature of tissue remodeling pathologies such as fibrosis and cancer. While genomic regulation downstream of normal mechanotransduction (i.e. cases where cells sense soft and stiff appropriately) is well studied, significantly less is known about the consequences of abnormal mechanoperception and subsequent misinterpretation of the mechanical environment.
Read the full summary ↓
Leveraging Thy-1 (a.k.a. CD90) loss as a model of impaired mechanoperception, we employed ATAC- and RNA-sequencing in parallel to characterize the changes in lung fibroblast genomic activity in response to a combination of substrate stiffness and culture time. Notably, we find perturbed mechanoperception elicits a near-complete shutdown of HOXA5, a transcription factor responsible for pattern specification and development in the nascent lung. In vitro investigation of HOXA5 expression reveals a potential mechanism connecting increased αv integrin signaling, cytoskeletal tension, and SRC kinase activity to HOXA5 silencing. These results establish novel links between integrin signaling and the expression dynamics of genes necessary for tissue formation and regeneration in the injured and/or developing lung, particularly HOXA5.
Published in
Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs
Miller AE, Hu P, Hannan RT et al. · PLoS genetics 2025 · PMID 41212903 · doi:10.1371/journal.pgen.1011924
This dataset
Open GSE292900 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE292900_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1241829 and SRA study SRP573090. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41212903) ↗
Study design
14 conditions, mostly with about 4 replicates each
WT, Suspension/0hr, ×4 WT, 4kPa substrate, 24hr culture, ×4 WT, 4kPa substrate, 72hr culture, ×4 WT, 25kPa substrate, 24hr culture, ×4 WT, 25kPa substrate, 72hr culture, ×4 WT, TCP substrate, 24hr culture, ×4 WT, TCP substrate, 72hr culture, ×4 Thy1-KO, Suspension/0hr, ×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

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