GEO series

Lung fibroblasts contribute to release of Serum Amyloid A as potential biomarker of exacerbation of lung fibrosis in mice [RNA-seq]

GSE318701 Mus musculus (mouse) Single-cell RNA-seq 32 samples Submitted 2026/03/05 Platform GPL21626

At a glance

Single-cell RNA-seq · mouse · 32 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: Mus musculus (mouse)
Samples: 32 samples
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)

Fibroblasts are important contributors to collagen deposition in interstitial lung diseases (ILD), but their inflammatory role in acute exacerbation of ILD including idiopathic pulmonary fibrosis (IPF) is currently undefined. Using a well described model of S.

Read the full summary ↓

pneumoniae (Spn) induced exacerbation of lung fibrosis in mice, we found that platelet-derived growth factor receptor A (PDGFRα) positive lung fibroblasts developed an early inflammatory phenotype upon infection including increased production of Serum Amyloid A (SAA) proteins, as determined by RNA sequencing, single-cell RNA sequencing and secretome profiling of sorted lung fibroblasts. Moreover, lung fibroblasts responded to pneumococcal challenge with increased SAA mRNA and protein levels in vitro. SAA levels were significantly elevated in BAL and plasma of mice with Spn-induced exacerbation of AdTGF-β1- or bleomycin-induced lung fibrosis. Antibiotic therapy caused a significant drop in SAA levels in BAL and plasma of mice with infection-driven fibrosis exacerbation. Finally, levels of SAA protein were dramatically increased in plasma of patients with acute exacerbation of interstitial lung disease (AE-ILD) but not in patients without exacerbation. We conclude that analysis of plasma levels of SAA protein may aid in the identification of underlying inflammation in patients with ILD who are more likely to deteriorate towards a critical clinical stage during acute exacerbation.

This dataset

Open GSE318701 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 GSE318701_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 PRJNA1419803 and SRA study SRP675236. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 32 more — browse all 32 samples with per-sample file links →

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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.