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Primary adventitial fibroblast response to TGFb is dependent on vascular site and implicates functional developmental epigenomic memory

GSE296074 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/07/29 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × Descending adventitial fibroblasts 0ng/ml TGFb, vs 3 × Descending adventitial fibroblasts 10ng/ml TGFb, vs 3 × Ascending adventitial fibroblasts 0ng/ml TGFb, vs 3 × Ascending adventitial fibroblasts 10ng/ml TGFb,Groups 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
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk lociMolecular systems biology · 2025
Summary (written by the submitters)
We have shown that vascular SMCs, fibroblasts, and endothelial cells have transcriptional and epigenomic features that are distinct to vascular site. Further, TF motif accessibility analysis in fibroblasts reveals an increased accessibility of AP1, and SMAD2:3:4, and TCF21 motifs in the ascending fibroblast population compared to carotid and descending fibroblasts, with further gene regulatory network analysis suggesting distinct regulatory TF module activity in ascending fibroblasts highlighting master regulator of fibroblast activation Meox1.
Read the full summary ↓
This differential chromatin accessibility would suggest the potential for heightened biological response to TGFb in ascending fibroblasts. To evaluate the functional effect of this differential chromatin accessibility and to identify if differential gene expression is retained following removal from vascular site flow conditions, we isolated and cultured primary adventitial fibroblasts from healthy 14 week old C57BL/6 mice from the ascending and descending aorta and stimulated them with control or TGFb (10ng/mL, 48hrs) and performed bulk RNA sequencing (n = 3 per condition).
Published in
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci
Weldy CS, Kundu S, Monteiro J et al. · Molecular systems biology 2025 · PMID 40931195 · doi:10.1038/s44320-025-00140-2
This dataset
Open GSE296074 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 GSE296074_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 PRJNA1257595 and SRA study SRP582667. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40931195) ↗
Study design
3 × Descending adventitial fibroblasts 0ng/ml TGFb, vs 3 × Descending adventitial fibroblasts 10ng/ml TGFb, vs 3 × Ascending adventitial fibroblasts 0ng/ml TGFb, vs 3 × Ascending adventitial fibroblasts 10ng/ml TGFb,

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
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