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.

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. 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.