Figure S6.

Power Calculations and Statistical Modeling of ACE2 Capture and Dropout Related to STAR Methods

(A). Probability of capturing and transcribing at least 1 ACE2 cDNA molecule, as a function of the capture/reverse transcription efficiency for a single molecule and the number of ACE2 molecules expressed in an individual cell. Note that Drop-Seq provides a capture/transcription efficiency of approximately 11-13%, setting a floor on this parameter, and the experimental platforms used in this study are either equivalent or superior (Macosko et al., 2015).

(B). Distribution of ACE2 fractional abundance within individual cells’ cDNA libraries (i.e., ACE2 UMIs / total number of reads), across non-human primate lung and ileum cell populations (see Figures 1 and 3). Mean fractional abundance among ACE2⁺ lung cells = 5.0E-5; mean fractional abundance among ACE2⁺ ileum cells = 2.7E-4.

(C). Distribution of the number of reads within non-human primate lung and ileum cell populations (see Figures 1 and 3). Mean ± SEM reads among all lung cells = 28,512 ± 344; ACE2⁺ lung cells = 28,553 ± 2,988; all ileum cells = 14,864 ± 288; ACE2⁺ ileum cells = 10,591 ± 441.

(D). Probability of observing at least one transcript for a gene of interest (e.g., ACE2) within an individual cell, as a function of sequencing depth and the gene’s fractional abundance (i.e., ACE2 reads / all reads) within the cell’s cDNA library. Fractional abundance provides the probability that a single read corresponds to the gene of interest, and presented heatmap indicates the probability that at least one read in the total number of reads allocated to the cell (i.e., from 10³ to 10⁶) originates from the gene of interest. Mean read depths and ACE2 fractional abundances for each tissue produce a 93.7% probability of detecting at least 1 ACE2 read in ileum cells, and a 76.0% chance for lung cells. Outlined rectangles highlight the regimes where cells from lung (turquoise) and ileum (pink) samples typically lie.

(E). Number of ACE2⁺ cells within each cluster, as a function of average read depth for all cells in that cluster. Number of cells detected as ACE2⁺ is not correlated with read depth, even across relatively wide ranges of average read depths (Pearson’s r = −0.31, n.s.).

(F). Probability of observing a particular number of cells positive for a gene of interest within a cluster, as a function of number of cells in the cluster. Probabilities were calculated under a negative binomial distribution with parameter p = 0.063 (the proportion of ACE2⁺ cells among type II pneumocytes presented in Figure 1; STAR Methods). The horizontal gray line indicates the arbitrary cut-off value of p = 0.05.

(G). Given a population of cells with a known proportion that are positive for a gene of interest, probability of observing no positive cells (i.e., false negative identification of the cluster; solid lines) and probability of observing at least one positive cell as a function of cluster size.