Extended Data Fig. 7: SP thymocytes are necessary for full cDC activation.
Related to Fig. 6. (a) RNA velocity analysis with arrows showing relative transition probabilities derived from ratio calculations of unspliced over spliced transcripts (cDCs -> aDCs). These analyses are consistent with differentiation trajectories of cDC1 to aDC1 and cDC2 to aDC2. (b) p-Creode analysis depicting cell-state transition trajectories for (left) cDC1 and (right) cDC2 transcriptional subsets, as in Fig. 6a,b. The topology was constructed with hierarchical placement, which connects the two transcriptionally closest end-states with path nodes. Overlay represents CytoTrace score to indicate cells with a high degree of stemness and transcriptional diversity (score closer to 1) versus those with a low degree of stemness, indicative of a more differentiated transcriptional state (score closer to 0). CytoTrace scores are consistent with more differentiated states of aDC1 and aDC2 relative to non-activated cDC1 and cDC2, respectively. (c) p-Creode (left) cDC1 and (right) cDC2 differentiation trajectories from WT and Rag2−/− scRNA-seq datasets overlaid with normalized expression values of select genes associated with cDC activation and licensing. (d) Violin plots showing normalized expression levels of the indicated genes, associated with DC activation or co-stimulation of T cells, from scRNA-seq data of WT versus Rag2−/− aDCs (combined aDC1, aDC2, and Il15rahi aDC clusters).
