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Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS.

GSE302019 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2026/01/06 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
Interleukin-7 receptor activation in interstitial macrophages promotes lung fibrosis through secreted phosphoprotein 1American journal of respiratory cell and molecular biology · 2026
Summary (written by the submitters)
This study aimed to characterize the transcriptomic landscape of Spp1-expressing interstitial macrophages (IMs) in the lungs of a bleomycin-induced pulmonary fibrosis mouse model using single-cell RNA sequencing (scRNA-seq). We utilized Spp1-EGFP knock-in reporter mice, in which EGFP marks Spp1-expressing cells. Pulmonary fibrosis was induced by intratracheal administration of bleomycin.
Read the full summary ↓
Lung cells were isolated, and Spp1-EGFP⁺ SiglecF⁻ CD11b⁺ interstitial macrophages were enriched by flow cytometric sorting. Approximately 10,000 viable sorted cells were processed for single-cell transcriptome profiling using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics), and libraries were sequenced on a DNBSEQ-G400 platform. This dataset provides a high-resolution view of the cellular states and gene expression profiles of interstitial macrophages during lung fibrosis.
Published in
Interleukin-7 receptor activation in interstitial macrophages promotes lung fibrosis through secreted phosphoprotein 1
Shirakawa K, Sano M, Sakane I et al. · American journal of respiratory cell and molecular biology 2026 · PMID 41092115 · doi:10.1165/rcmb.2025-0254OC
This dataset
Open GSE302019 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 GSE302019_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 PRJNA1286126 and SRA study SRP598424. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41092115) ↗
Study design
8 conditions, mostly in triplicate
WT C57BL/6J, PBS day 7, CD11b+ SiglecF- macro… ×3 WT C57BL/6J, Bleomycin day 7, CD11b+ SiglecF-… ×3 Spp1-EGFP KI reporter mice, Bleomycin day 7, … ×3 Spp1-EGFP KI reporter mice, Bleomycin day 7, … ×3 Spp1-EGFP KI reporter mice, Bleomycin day 14,… ×3 Spp1-EGFP KI reporter mice, Bleomycin day 14,… ×3 Spp1-EGFP KI reporter mice, Bleomycin day 30,… ×3 Spp1-EGFP KI reporter mice, PBS day 7, Spp1-E… ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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