Figure S1.

NHP Tuberculosis Infected Lung and Granuloma, Related to Figures 1 and 2

(A). UMAP projection of epithelial cells (1,099 cells) colored by annotated cell type, tissue source, and gating as ACE2⁺TMPRSS2⁺ cells. ACE2⁺TMPRSS2⁺ cells comprise 11% of ciliated cells, 16% of club cells, 10% type I pneumocytes, and 22% type II pneumocytes. Data generated using Seq-Well S³ (Table S3).

(B). Number of cells (left) and % (right) ACE2⁺TMPRSS2⁺ cells by tissue source (granuloma versus uninvolved lung) and cell type. Ciliated cells and club cells were omitted from this analysis as we detected too few cells (< 7 total cells) belonging to these clusters in the granulomas. Statistical significance assessed by Fisher Exact Test (Table S3).

(C). Dot plot of top cluster defining genes for each epithelial cell type and ACE2 and TMPRSS2. Dot size represents fraction of cells expressing, and color intensity represents average log(normalized UMI + 1) among all cells in each group scaled between 0 and 1 by gene. ACE2 expression is enriched in club cells (Bimodal test, Bonferroni-corrected p < 0.001), ciliated cells (p < 0.005), and type I pneumocytes (p < 0.001). TMPRSS2 expression is enriched in type I pneumocytes (p < 0.001) and ciliated cells (p < 0.001) (Table S3).

(D). Dot plot of genes differentially expressed between ACE2⁺TMPRSS2⁺ epithelial cells versus rest (Bimodal test, Bonferroni-corrected p < 0.01, log fold change > 0.5). (Table S3, c = number of cells, n = number of animals).