Extended Data Fig. 2: Cell-type annotation for the endothelial lineage using UMAP plots and spatial data.

a, Lineage-level UMAP for endothelial cells generated after final cell-type annotation. Cell types are colored based on the legend in b. b, Proportion of the total number of endothelial cells by disease state (unaffected, less affected or more affected). Capillary cells are the majority endothelial cell type in unaffected samples, but capillary cells are lost in PF. c,d, Select cell-type gene markers visualized in UMAP space across all endothelial cells (c) and split by cell type (d). e, An example spatial plot of sample VUILD107MF (IPF diagnosis). Each point represents a cell, colored by cell type. Smooth muscle cells (SMCs)/pericytes of the mesenchymal lineage are included to provide additional spatial context for the location of endothelial cells. f, Plots of the same sample showing expression of select endothelial cell marker genes. Only endothelial cells are included in these plots. For d and f, boxes indicate the cell type of the gene marks. Gray-dashed lines indicate general endothelial lineage markers.