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Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis

GSE288947 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2025/07/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 13 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
13 samples: 7 × FFPE lung slides BLM-treated mouse, Day21, sample vs 6 × FFPE lung slides control mouse, Day21, sampleGroups 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
Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosisRespiratory research · 2025
Summary (written by the submitters)
RNA sequencing can provide insightful information on the molecular processes underlying development and progression of multiple diseases, including idiopathic pulmonary fibrosis (IPF) and its bleomycin (BLM)-induced preclinical model. We investigated the feasibility of applying RNAseq analysis to formalin-fixed and paraffin-embedded (FFPE) lung slides from control and BLM-treated mice.
Read the full summary ↓
The results were validated by comparison with public bulk data from fresh-frozen mouse tissue and human IPF biopsies. Unsupervised cluster analysis on Differentially Expressed Genes revealed gene clusters associated with extracellular matrix organization, tissue remodeling and inflammatory response pathways, distinguishing untreated and BLM-treated fibrotic lung samples. For each sample, expression levels of individual gene clusters were highly correlated with 2D histology readouts and aeration compartments determined on matched 2D coronal slices by micro-CT imaging. This combined approach can produce a precise, spatially oriented picture of pulmonary disease development, paving the way to the identification of novel translationally relevant biomarkers and therapeutic targets.
Published in
Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis
Ferrini E, Bonfini C, Marchese G et al. · Respiratory research 2025 · PMID 40604969 · doi:10.1186/s12931-025-03300-y
This dataset
Open GSE288947 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 GSE288947_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 PRJNA1220076 and SRA study SRP562077. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40604969) ↗
Study design
7 × FFPE lung slides BLM-treated mouse, Day21, sample vs 6 × FFPE lung slides control mouse, Day21, sample

Supports a case/control comparison: 7 samples read as cases, 6 as controls.

How we read this: 2 replicated groups read from 13 sample titles; they account for 13 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
Datasets on a similar topic

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