Fig. 6: Trajectory analysis predicts supporting cell to hair cell transition.

a CellRank cell-cell transition matrix trajectory plot showing hair cell precursors differentiating towards mature hair cells (most arrows pointing to the left). b SWNE plot with projected type I and type II hair cell lineages and predicted hair cell precursors (cluster 7, pink). c Diagram showing supporting cells transition to hair cell-like cells through hair cell precursors. d, e Heatmap depicting dynamically expressed genes along the type I and II hair cell lineages (9731 and 4315 genes, respectively, FDR ≤ 0.01). There are five patterns of dynamic expression with some genes upregulated, some downregulated, and others transiently expressed in both type I and II lineages. (d: 1, 3 = up, 2 = down, 4, 5 = transient, e: 1, 5 = up, 2, 4 = transient, 3-down/transient) (colors correspond to the Source Data file). The density of cells, number of cell clusters, and corresponding location along the lineage is depicted below the heatmap. f, f’ Plots showing the dynamic expressions of genes from (d, e) that increase (left column) or decrease (middle column) along pseudotime. The individual dots in each plot represent single cells (cyan represents supporting cells, magenta represents hair cell precursors, purple and green showing type I and type II hair cells, respectively) with the x-axis representing pseudotime and the y-axis showing log₂ expressions. The solid line represents the generalized additive model fit to the expression pattern for each gene. f” Comparison of type I versus type II hair cell dynamic gene expressions. Using the different end test, we detected statistically significant genes that begin at similar expression levels and end at different levels. SOX2, CXCL14, and CSRP2 expression increase in type II hair cells, while ADAM11, VSIG10L2, and ESPN increase in type I hair cells. g Graph showing eight top scoring canonical pathways associated with the type I and/or type II lineages along with the corresponding percentage of significantly expressed genes relative to the total number of genes in each pathway. h Graph of top biological function GO terms associated with type I and type II lineages. Source data are provided as a Source Data file.