Trajectory analysis of scRNA-seq neonatal lung ILC2s identifies effector ILC2 subsets and ILC progenitor-like cells in the neonatal lung. (A) A single-cell trajectory was constructed from the neonatal ILC2 dataset in Fig. 4 D using the Monocle package, and neonatal ILC2s were ordered in pseudotime along a tree-like differentiation trajectory. Five distinct segments or states of the trajectory were identified. (B) Heatmap of the expression of ILC2-associated genes in the indicated states in A. (C) Changes in the expression of the indicated ILC2-associated genes along cell fate progression in pseudotime, from state 1 to states 4 and 5 in A. (D) The cells from states 1, 4, and 5 were combined and subjected to further unsupervised clustering using Seurat package, which divided them into three distinct subsets, namely ILCP (95 cells), proinflammatory (175 cells), and tissue-repairing (247 cells) ILC2 subsets. Heatmap shows top 20 genes that are differentially expressed by the subsets. The arrows point to the genes that are mentioned in the text.