Extended Data Fig. 6: Additional analysis of skin ILC trajectories and of differential gene expression in ILC3-like cells originating along different trajectories.

a–d, Additional visualizations for trajectories identified by directed diffusion (as in Fig. 2b). For the cloud-to-ILC3-like trajectory: FDL embedding (as in Fig. 2a) with cells (dots) in the trajectory highlighted in blue for each day (panel title, cells not inferred to be in the trajectory or from other days in grey) (a), and heatmap of co-expression (top) and normalized expression (bottom; colour bar: low, grey; high, burgundy) of trajectory-associated genes (rows) in cells (columns) ordered by pseudotime (colour bar, top) (b). Analogous plots are shown for the potentially bidirectional ILC2-to-quiescent-like trajectory (c, d). e–h, Distinct trajectories leading to ILC3-like cells are characterized by differentially expressed genes (Methods). FDL embedding (as in Fig. 1e) including all cells (e), and cropped to focus on ILC3-like cells (f), shows cell profiles (dots), coloured by normalized expression (colour bar: low, grey; high, maroon) of genes (panels) more highly expressed by ILC3-like cells in the ILC2-to-ILC3-like trajectory (as in Fig. 2b, e–f) than by other ILC3-like cells, including Bcl2a1b, which is specifically low in quiescent-like cells, compared to other ILCs. Analogous plots are shown for genes with higher expression in the quiescent-to-ILC3-like trajectory, compared to other ILC3-like cells (g, h). P values in Supplementary Table 4.