Extended Data Fig. 7: Reference based integration of primary epithelium and hES cell derived epithelial populations.

A) UMAP analysis showing the distribution of primary human epithelial populations within the concatenated data set of primary human epithelium, iRAS cells, and iAT2 cells. Grey cells represent non-primary human cells (ES derived populations). Colors correspond to primary human cell populations as indicated. All primary epithelial populations are shown. B) UMAP showing distribution of the hES cell populations included in the concatenated data set. Colors correspond to hES cell populations based on gene expression of SCGB3A2 and SFTPC as indicated. C) Percentage of hES cells within primary cell defined clusters within concatenated data set. Clusters were identified based on localization of primary human epithelium. D) Venn diagram of Transcription factors identified as upregulated in primary RAS  and iRAS cells compared to primary AT2 and iAT2 cells, respectively. E) Expression of Notch pathway genes HES1 and HES4 in primary RAS and iRAS cells compared to AT2 cell counterparts. F) Reference based integration of primary adult human epithelium, fetal human lung epithelial from day 11.5, 15, 18, and 21 (the days which included SCGB3A2+ secretory cell progenitor populations) from published fetal lung data set³², and iRAS cells. All three SCGB3A2+ populations clustered together, and SCGB3A2+ cells are shown in red. G) SCGB3A2+ cells were selected and re-clustered. H) A stacked bar graph of the contribution of each population to each resultant cluster.