GEO series

Characterisation of a pathogenic non-migratory fibroblast population in systemic sclerosis skin

GSE292702 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/10 Platform GPL18573

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. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: Characterization of a pathogenic nonmigratory fibroblast population in systemic sclerosis skinJCI insight · 2025

Summary (written by the submitters)

Fibroblasts are central to pathogenesis of systemic sclerosis (SSc). However, studies of conventional explant fibroblast cultures incompletely reflect disease biology and treatment response. We isolated a second non-migratory “resident” population of fibroblasts from skin biopsies after outgrowth of explant “migratory” cells. These non-motile resident fibroblasts were compared with migratory cells from the same biopsy, using functional studies, bulk and scRNAseq, and localised in situ by multichannel immunofluorescence.

Read the full summary ↓

Migratory and resident fibroblast populations in SSc showed distinct pro-fibrotic characteristics and gene expression for pathogenic pathways differing by stage and autoantibody subgroup. TGFβ signalling was highly active in migratory fibroblasts in early stage dcSSc. Conversely, resident fibroblasts had less upregulated TGFβ signalling, especially in late dcSSc. Increased chemokine expression was a hallmark of resident fibroblasts at all stages. In vitro studies confirmed differential response to TGFb1 and CCL2 between migratory and resident cells. We suggest that migratory fibroblasts are especially important in early skin disease whereas non-migratory fibroblasts may have a regulatory role and contribute more to fibrosis in later stage disease. Thus, we have identified a pathogenic fibroblast population in SSc, not isolated by conventional explant culture, that could play an important role in fibrosis and be targeted therapeutically.

Published in

Characterization of a pathogenic nonmigratory fibroblast population in systemic sclerosis skin

Clark KE, Xu S, Attar M et al. · JCI insight 2025 · PMID 40232859 · doi:10.1172/jci.insight.185618

This dataset

Open GSE292702 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 GSE292702_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 PRJNA1241113 and SRA study SRP572863. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40232859) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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

GSM8863845 HC1 early
GSM8863846 HC1 res
GSM8863847 HC2 early
GSM8863848 HC2 res
GSM8863849 HC3 early
GSM8863850 HC3 res
GSM8863851 SSc1 early
GSM8863852 SSc1 res
GSM8863853 SSc2 early
GSM8863854 SSc2 res
GSM8863855 SSc3 early
GSM8863856 SSc3 res

Datasets on a similar topic

GSE292979 Characterisation of a pathogenic non-migratory fibroblast population in systemic sclerosis skin [scRNA-Seq] 15 samples shares non-migratory, pathogenic, fibroblast, population, sclerosis, systemic, skin
GSE320020 Macrophage–Fibroblast Signaling Network Identified by Single-Cell RNA Sequencing in Juvenile Systemic Sclerosis 11 samples shares fibroblast, sclerosis, systemic
GSE330762 Kabuki syndrome type I fibroblast multi-omics dataset: bulk RNA-seq profiles from primary skin fibroblasts 19 samples shares fibroblast, skin
GSE301908 Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesions - snRNA-seq 17 samples shares pathogenic, sclerosis
GSE269317 Reduced WNT4 expression in normal skin fibroblasts leads to ‘Dupuytren-like’ changes in the transcriptome 16 samples shares fibroblast, skin
GSE231998 The use of ectopic volar fibroblasts to modify skin identity 49 samples shares fibroblast, skin
GSE312129 Single-nuclei multiome and spatial analyses of early, untreated SSc skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling 38 samples shares fibroblast, skin
GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 samples shares fibroblast

Search all human RNA-seq datasets in GEO →

Share this dataset

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.