scRNA-seq analyses of iNs and other cells.

(A) UMAP combining all 9 samples: WT, Per1-/-, and Per2-/- cells on days 4, 7, and 10. (B) Dot plot showing top 3 marker genes in each cluster. (C) Temporal profiles of the proportions of 6 clusters. (D) Violin plots depicting the expression levels of neuronal genes in neuronal clusters. (E) GSEA of more highly (red) or lowly (blue) represented genes in Per1-/- macrophages than in WT and Per2-/- macrophages on day 7. (F) Heatmaps of the genes in the TNFα and IL-6 signaling pathways up-regulated in Per1-/- cells in (E). (G) Heatmap of axon guidance genes common to the top and bottom panels in (E).* p p n = 1 for each sample. GSEA, Gene Set Enrichment Analysis; iN, induced neuron; scRNA-seq, single-cell RNA sequencing; UMAP, uniform manifold approximation and projection; WT, wild-type.