Figure 3: Distinct populations can be detected in fresh 68k PBMCs.

(a) Distribution of number of genes (left) and UMI counts (right) detected per 68k PBMCs. (b) tSNE projection of 68k PBMCs, where each cell is grouped into one of the 10 clusters (distinguished by their colours). Cluster number is indicated, with the percentage of cells in each cluster noted within parentheses. (c) Normalized expression (centred) of the top variable genes (rows) from each of 10 clusters (columns) is shown in a heatmap. Numbers at the top indicate cluster number in (b), with connecting lines indicating the hierarchical relationship between clusters. Representative markers from each cluster are shown on the right, and an inferred cluster assignment is shown on the left. (d–i) tSNE projection of 68k PBMCs, with each cell coloured based on their normalized expression of CD3D, CD8A, NKG7, FCER1A, CD16 and S100A8. UMI normalization was performed by first dividing UMI counts by the total UMI counts in each cell, followed by multiplication with the median of the total UMI counts across cells. Then, we took the natural log of the UMI counts. Finally, each gene was normalized such that the mean signal for each gene is 0, and standard deviation is 1. (j) tSNE projection of 68k PBMCs, with each cell coloured based on their correlation-based assignment to a purified subpopulation of PBMCs. Subclusters within T cells are marked by dashed polygons. NK, natural killer cells; reg T, regulatory T cells.