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Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis

GSE309471 Mus musculus (mouse) Single-cell RNA-seq 46 samples Submitted 2025/11/03 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 46 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
46 samples: 16 conditions, mostly in duplicateGroups 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
Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor-CD74 signalingScience translational medicine · 2025
Summary (written by the submitters)
This study aimed to elucidate how epithelial–macrophage interactions contribute to pulmonary fibrosis. Using bleomycin-induced and genetic mouse models (Mif-2 KO, SPC-Cul3 KO, SPC-Mif KO, CX3CR1-Cd74 KO, PF4-Cd74 KO, and TGF-β transgenic mice), we performed single-cell transcriptomic profiling of lung cells and compared them with wild-type controls.
Published in
Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor-CD74 signaling
Kim SH, Nouws J, Ruwisch J et al. · Science translational medicine 2025 · PMID 41337540 · doi:10.1126/scitranslmed.adr2277
This dataset
Open GSE309471 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 GSE309471_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 PRJNA1336137 and SRA study SRP629466. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41337540) ↗
Study design
16 conditions, mostly in duplicate
CX3CR1-Cd74-WT-Bleoymcin ×4 CX3CR1-Cd74-KO-Bleoymcin ×3 SPC-Mif-WT-Bleomycin-D14 ×3 SPC-Mif-KO-Bleomycin-D14 ×3 PF4-Cd74-KO-Bleoymcin-D14 ×3 TGF WT-C ×3 TGF-Tg ×3 DDT WT-Control ×2 +14 more

Supports a between-group comparison across 40 samples.

How we read this: 16 replicated groups read from 46 sample titles; they account for 40 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

Search all mouse 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.