IMC raw data: spatial immune-stromal profiling in bleomycin-induced pulmonary fibrosis mouse model

This dataset contains raw Imaging Mass Cytometry (IMC) data files (.mcd) acquired from lung tissue sections of a bleomycin (BLM)-induced pulmonary fibrosis mouse model. The data were generated to investigate the spatial immune-stromal interactions and cellular landscape heterogeneity between pulmonary fibrosis (PF) regions and inflammatory pulmonary (IP) regions within the same BLM-injured mouse lungs. Pulmonary fibrosis was induced in mice via intratracheal administration of bleomycin, and lung tissues were harvested at day 14 post-induction. Hematoxylin and eosin (H&E) staining was performed to identify two distinct pathological regions within the same BLM-treated lung sections: (1) pulmonary fibrosis (PF) regions, characterized by dense collagen deposition, myofibroblast proliferation, and alveolar structural collapse; and (2) inflammatory pulmonary (IP) regions, characterized by extensive inflammatory cell infiltration, thickened alveolar walls, and relatively preserved alveolar cavity structures. Three PF regions of interest (ROIs) and three IP ROIs were selected from each BLM mouse lung tissue section for IMC acquisition. The dataset includes three samples (one per BLM-treated mouse): IMC_20260319_T001_D75_MLT_A_6R.mcd (lung tissue section D75 from BLM mouse #1, containing 6 ROIs [3 PF + 3 IP]); IMC_20260320_T002_D76_MLT_A_6R.mcd (lung tissue section D76 from BLM mouse #2, containing 6 ROIs [3 PF + 3 IP]); and IMC_20260320_T003_D77_MLT_A_6R.mcd (lung tissue section D77 from BLM mouse #3, containing 6 ROIs [3 PF + 3 IP]). In total, 18 ROIs (9 PF + 9 IP) were acquired across 3 biological replicates, yielding 91,785 single cells for downstream analysis. The IMC antibody panel comprises 31 metal-tagged antibodies across seven functional categories: (1) epithelial/endothelial markers (Pan-CK, CD31); (2) mesenchymal/stromal markers (α-SMA, Vimentin, Collagen I); (3) myeloid markers (CD45, CD68, CD11b, CD11c, F4/80, Ly6G, MHCII, CSF1R, CD103); (4) T cell subsets (CD4, CD8, CD45R, FoxP3, Granzyme B); (5) immune checkpoint markers (PD-L1, PD-1, TIM3, CD38); (6) functional/signaling markers (Ki67, STAT3, VEGFA, CD44, Plaur); and (7) senescence markers (p21, CDKN2A). Data acquisition was performed using the Hyperion Imaging System (Standard BioTools, formerly Fluidigm) on formalin-fixed paraffin-embedded (FFPE) lung tissue sections, with ROI selection guided by H&E staining-based pathological classification (PF vs IP). The raw .mcd files contain single-cell resolution spatial proteomics data with ion intensity per metal tag channel. Raw .mcd files were processed using the following pipeline: MCD Viewer (Standard BioTools) for image extraction and quality control; CellProfiler for cell segmentation; histoCAT v1.76 for single-cell expression matrix generation; R/Seurat for unsupervised clustering (PhenoGraph), dimensionality reduction (UMAP), and cell type annotation; and custom R scripts for spatial analysis including cellular neighborhood (CN) classification, cell-cell interaction analysis, and differential abundance testing. Paired statistical comparisons between PF and IP regions were performed at the mouse level (n = 3 mice).