Libraries corresponding to 10 animals (variable number of tissues/animal) were sequenced using Illumina NovaSeq S2. Data was aligned using the Dropseq-tools pipeline on Terra (app.terra.bio) to M. fascicularis reference genome assembly 5, annotation version 101. Clustering was performed using Leiden clustering in the Scanpy (scanpy.readthedocs.io) package (Wolf et al., 2018). Cell type labels were assigned using known marker genes. In this analysis, we include all epithelial cell subsets (secretory, multiciliated, type II pneumocytes, and type I pneumocytes) from all samples. Differential expression between ACE2 + TMPRSS2 + cells and other cells of the matched cell subtype (e.g., Secretory Cells) were performed using the “bimod” likelihood-ratio test within each cell subtype and filtered on Benjamini-Hochberg-corrected p value < 0.05. Expression data for epithelial cells included in this dataset can be visualized and downloaded here: