Extended Data Fig. 11: All COPD patients contributed to all resultant clusters and gene expression within the COPD epithelium highlights the various epithelial cell clusters.

Each patient contribution is shown overlying the entire concatenated UMAP for A) the entire data set (top row), and the subset of epithelial cells (bottom row). B) Stacked bar graph showing the patient contribution to each epithelial cell cluster, demonstrating that all patients contributed to all resultant clusters. RAS cell cluster marked with red asterisk. C) Canonical marker genes used to identify epithelial clusters are shown. D) Violin plots demonstrate distribution of known canonical marker genes across the various epithelial populations. E) Cluster defining genes within the COPD epithelium are shown in dot plot format. There are distinct changes in the transcriptome of non-epithelial populations in COPD. GO analysis of inter-cluster gene expression comparing select endothelial (F) and mesenchymal (G) populations suggests that the differential gene expression seen in the epithelium is distinct to that population.