Extended Data Fig. 5: Trajectory of primary human proximal and distal epithelium demonstrates both anticipated and novel epithelial progenitor relationships.

A) Proximal airways epithelium clustering and resultant cell populations shown for reference for following analysis. B) Trajectory analysis in the proximal human airways results in 3 putative lineage relationships. UMAP plots show trajectories, color represents cell localization along pseudotime. Heatmaps showing expression of trajectory defining genes across pseudotime. C) Trajectory analysis of scRNAseq gene expression across distal epithelial populations suggests several epithelial relationship, including D) a putative relationship between RAS cells and AT2 cells. E) Heatmap of defining gene expression changes along pseudotemporal ordering of cells from RAS cell-to-AT2 cell trajectory. Pseudotemporal ordering shown in bar above heatmap. F) Additional epithelial trajectories were identified by slingshot analysis within the distal epithelium. For the additional trajectories that are not a focus of this current study, the individual trajectory is shown along with the corresponding heatmap of trajectory defining genes. Top indicated position along trajectory as color coded by position of the cell along pseudotemporal ordering. G) Gene expression in UMI count of selected genes along pseudotemporal ordering of distal trajectory 1 (panel d, e) on the x-axis.