Extended Data Fig. 12: Epithelial cell gene expression differences in disease and the RAS cell to AT2 cell transition is altered in COPD.

A) Concatenation of normal and COPD peripheral samples and subset of epithelium showing expected epithelial populations. B) Identification of RAS cell and SCGB3A2+ AT2 populations based on expression of markers indicated. C) GO analysis of intra-cluster gene expression of RAS cells comparing COPD and healthy patient derived cells. D) Violin plots of selected genes contributing to GO processes in (C). E) GO analysis of inter-cluster gene expression comparing SCGB3A2+ AT2 cells from COPD donors and AT2 cells from healthy donors and F) corresponding selected gene expression. G) GO analysis of intra-cluster gene expression of AT2 cells from COPD and healthy controls. H) Violin plots of selected genes from GO processes in (G). For all, up regulated is COPD compared to healthy controls. I)Transcriptional inference analysis of the concatenated data set revealing multiple trajectories initiating at RAS cells. J, K) Comparison of gene expression along trajectory 1 (T1) versus trajectory 2 (T2) demonstrating differential gene expression changes along pseudotemporal ordering between the RAS to AT2 cell trajectory and the RAS to SCGB3A2+ AT2 cell trajectory. L) Distribution of individual patient data is shown overlaying concatenated UMAP of the COPD and healthy peripheral data sets. All cells are shown in top two rows, and epithelial subsets in bottom rows. M) Stacked bar graphs highlight patient level contribution to each cluster. RAS cells are indicated in red asterisk.