Fig. 4

Integration of CyTOF and scRNA data of CD19-CAR NK, IL15 NK, and NT-NK cells. a, b Cells from CD19-CAR NK, IL15 NK, and NT-NK products, clustered independently by CyTOF (a) and scRNA (b) data. There is no correspondence between protein clusters (pClusters) and RNA clusters (rClusters). c, d Integrated clusters (iClusters) after running bindSC on the CyTOF and the scRNA data. CyTOF (a) and scRNA-seq (b) are emphasized, respectively, for better visualization. Cells in the non-emphasized modality are shown in light gray. iCluster 2 is circled out by dashed lines. e Correspondence of iClusters and rClusters. The colors denote the proportion of iCluster in each protein cluster, normalized by each column. The top annotation shows frequencies of three cell groups (cyan: NT-NK, blue: IL15, green: CD19) in each iCluster. f Differentially expressed (Wilcoxon test) genes between iCluster 2 and iClusters 3 and 4. Highlighted genes are known NK cell activation (upregulated). g Gene expression levels of CCL4 and CCL3 in iCluster 2 and rClusters R0 and R2. The p values shown are from the Wilcoxon test. h Protein expression levels of 2B4 and DNAM-1 in iCluster 2, 3, and 5. The p values shown are from the Wilcoxon test