Fig. 2: Distribution of non-epithelial cell subtypes in histological tissue compartments.

A Heatmap of average (mean) cell type proportions (%) in manually annotated histological compartments using HybISS cell type maps. Proportion calculations include non-annotated cells, not presented in the heatmap. Cell type/subtype maps on top of nuclei (DAPI, white) of HybISS (left) and SCRINSHOT (right) datasets of donor 1 trachea (B) and distal lung (C), respresentative images from four biological replicates. Dotted outlines: peribronchial and airway (AW), submucosal gland (SMG), alveolar (Alv) and arterial (Art) compartments. Cell type abbreviations: pb peribronchial, adv adventitial, alv alveolar, pv perivascular, cap capillary, gen general, art arterial, ven venous, nan not annotated. Scale bar 200 µm. D Graph of mean cell type/subtype proportions in each of the peri-epithelial compartments. Floating bars indicate Min/Max values as bounds of box, with a line on mean proportion per compartment, and indicated in percent (%), n = 3 in tracheal regions, n = 4 in proximal and distal lung regions. Values were compared in lung regions using Friedman two-sided test followed by Dunn’s multiple comparisons test. Significant differences (P < 0.05) are indicated by asterisk (*). Adjusted P values are as follows: P = 0.0370 for fibroblasts (RGCC) between alveolar parenchyma and proximal bronchi; P = 0.0370 for smooth muscle cells between alveolar parenchyma and proximal bronchi; P = 0.0370 for endothelial (CLDN5) cells between alveolar parenchyma and proximal SMG. The cell subtypes that dominated in one anatomic location are highlighted with coloured boxes. E Schematic summary of the gene expression in the parenchyma of each compartment. Source data are provided as a Source Data file.