Fig. 1

Single-cell transcriptome map of thymocytes. a Schematic of procedures for the extraction, sequencing, and single-cell analysis of thymocytes. b Two-dimensional representation of cells via t-SNE, as colored by cluster identity; each dot represents one cell. t-SNE was performed after quality control. c Two-dimensional representation of cells via tSNE, as colored by the PBA-predicted differentiation order (see “Methods”); each dot represents one cell. d Heat map of cluster marker genes (color-coded by clusters), with representative genes labeled (right). Columns denote cells; rows denote genes. e Il2ra, Cd4, Cd8a, Mki67, Rag1, Itm2a, Ccr7, Klrd1 and H2-Aa marker genes projected onto t-SNE plots. Color bar, normalized expression value