Figure 3.

Pseudotime trajectory of the differentiation paths for NPC-derived cells and cell-to-cell communication patterns

(A) Pseudotime trajectory analysis of NPC-derived neuronal, astrocyte, and oligolineage cells, colored by Seurat cell cluster for doxycycline-untreated vs. treated organoids.

(B and C) Hierarchical clustered heatmap depicting genes whose expression patterns covary across pseudotime (Z scores normalized by row) at branchpoints 1 and 2, respectively, for doxycycline-stimulated organoids.

(D) Pseudotime trajectory analysis of selected NPC-derived neuronal (NEU) (cluster 3 and 10), astrocyte (ASTRO) (cluster 4 and 6), and OL (cluster 16), showing the high degree of their maturation, and cycling cells (CYCLING) (cluster 7), colored by pseudotime, for doxycycline-untreated vs. treated organoids.

(E) Immunostaining of SOX10⁺ and MBP⁺ cells in cryosections at 2, 5, 8, and 16 weeks of differentiation in doxycycline-exposed SOX10-eGFP organoids (scale bar: 30 μm).

(F) Circle plot representing cellular communication among the different clusters in organoids using CellChat. Circle sizes are proportional to the number of cells in each cell group and edge width represents the communication probability.

(G) Heatmap showing detailed communication through individual pathways and providing insights into the autocrine- vs. paracrine-acting pathways for each cell type using CellChat.