Extended Data Fig. 1: Single-cell multi-omics profiling of pre-infusion CAR T cells.
From: Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission
a, Experimental pipeline of this study. b, Cell proportion in each identified cluster, and the ratio of CD4+ and CD8+ cells in each stimulation condition determined by CITE-seq surface protein data. c, UMAP distribution of all the single cells grouped by in vitro stimulation condition (upper panel) or cell cycle (lower panel). d, Expression of surface protein ADT-CD69 (activated T cell marker), ADT-CD62L (naïve T cell marker), ADT-CD4 and ADT-CD8 (subtype T cell marker) on the UMAP. e, UMAP distribution of 695,819 single CAR T cells split by sequencing batch, suggesting minimum batch effect. f–m, Expression distribution of memory states (f), Th1/Tc1 (g), Treg (h), Th2/Th9/Th17 (i), selected chemokines (j), cytotoxicity (k), cell cycle (l), and other (m) gene markers on the UMAP shown in Fig. 1b. n, CAR T cell signatures within each identified cluster based on cell states, functions, regulations, or subsets. The heatmap illustrates the averaged expression of curated T cell marker genes in each cluster. o, Heatmap showing the average expression level of ADT proteins of all the single cells in each identified cluster.
