Fig. 4: Cluster-specific gene expression reveals the relationships among the wild-type clusters.

a A heatmap showing the top ten enriched genes in each cluster. Each horizontal line represents one gene and each vertical line represents one cell. Data from equal numbers (100) of cells from each cluster are shown. The heatmap demonstrates the continuity and directionality between these clusters. The color scale represents relative expression levels which were generated by averaging the normalized gene expression values in each cluster and then centering and scaling the values in each row using R bioconductor package “pheatmap” (see “Methods”). b A Venn diagram showing the overlaps of enriched genes between naive RPCs (nRPC, C0–C2), transitional RPCs (tRPC, C3 and C4), and retinal ganglion cells (RGCs, C5 and C6). tRPCs have substantial overlaps with both nRPCs and RGCs, but nRPCs and RGCs have very few overlapped genes, indicating the unidirectional relationship of these clusters. Source data are provided in Supplementary Data 4. c, d Developmental trajectories predicted by the SCANPY tool based on diffusion pseudotime (DPT), which measures transitions between cells (see “Methods” for details). The color scales represent estimated DPTs for individual cells, where 0 is the start pseudotime, and 1 is the end pseudotime. Three trajectories representing the emergence of photoreceptors (PH), horizontal and amacrine cells (H&A), and RGCs from RPCs are identified for both the wild-type (WT) (c) and Atoh7-null (MT) (d) cells. The direction of each lineage is clearly discernible, although the RGC lineage of the MT cells does not advance as far as the WT cells.