GEO series

Transcriptional and spatial profiling of fibroblasts from human lungs highlights CTHRC1+ cells as fibrogenic signaling hubs in fibrosis

GSE331144 Homo sapiens (human) Single-cell RNA-seq 9 samples Submitted 2026/05/29 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 9 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: 9 samples: 9 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.

Summary (written by the submitters)

This dataset contains single-cell RNA sequencing (scRNA-seq) data from native human lung tissue obtained from idiopathic pulmonary fibrosis (IPF) patients and age-matched controls. Samples were collected from IPF upper lobe, IPF lower lobe, and age-matched control lung tissue and processed using the 10x Genomics Chromium platform. Unsupervised clustering identified six transcriptionally distinct mesenchymal subtypes — alveolar, adventitial, inflammatory, CTHRC1⁺, peribronchial and smooth muscle cell — across conditions.

Read the full summary ↓

Differential gene expression, pathway enrichment, and cell-cell communication analyses were performed to characterize subtype-specific transcriptional programs, ECM remodeling signatures, and intercellular signaling networks in the fibrotic lung niche. CTHRC1⁺ fibroblasts emerged as a dominant fibrogenic hub in IPF, characterized by elevated fibrillar collagen expression, broad outgoing signaling through collagen, fibronectin, and periostin pathways, and spatial co-localization with fibroblastic foci. This dataset provides a transcriptional resource for investigating mesenchymal heterogeneity and fibrogenic cell states in human pulmonary fibrosis.

This dataset

Open GSE331144 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 GSE331144_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 PRJNA1460788. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 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 9 sample titles: 9 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

GSM9739687 S1_A001_Healthy_lung_parenchyma
GSM9739688 S2_U160_IPF_lung_upperlobe_replicate1
GSM9739689 S3_U161_IPF_lung_upperlobe_replicate2
GSM9739690 S4_U172_IPF_lung_upperlobe_replicate3
GSM9739691 S5_U183_IPF_lung_upperlobe_replicate4
GSM9739692 S6_U197_IPF_lung_upperlobe_replicate5
GSM9739693 S7_U001_IPF_lung_upperlobe_replicate6
GSM9739694 S8_U010_IPF_lung_upperlobe_replicate7
GSM9739695 S9_L197_IPF_lung_lowerlobe_replicate8

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GSE272972 Critical role for the TGF-β1/mTORC1 signalling axis in defining the transcriptional identity of CTHRC1+ pathologic fibroblasts in idiopathic pulmonary fibrosis 18 samples shares cthrc1, fibroblasts, fibrosis
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GSE322964 Single cell and spatial sequencing analysis of cancer associated fibroblasts in the brain metastasis tumor microenvironment [Multiome] 22 samples shares fibroblasts, spatial
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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 fibroblasts
GSE297400 Transcriptome Profiling of Human Dermal Fibroblasts Treated with 4 Phosphodiesterase Inhibitors Across Multiple Dose Gradients 199 samples shares fibroblasts
GSE298908 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq] 113 samples shares fibroblasts

Search all human RNA-seq datasets in GEO →

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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.