Fig. 5: Spatial expression of Sox4 and Sox11.

a, b Feature plot heatmaps indicate that both genes are expressed in all clusters but at much higher levels in differentiating cells, and that their expression levels are comparable in wild-type (WT) and Atoh7-null (MT) cells. Color scales represent natural-log transformed normalized gene expression levels as described in “Methods”. c Violin plots indicate that both genes are expressed in comparable levels in corresponding WT (red) and MT (blue) clusters. The heights of the plots represent expression levels as described in “Methods” and the widths represent relative proportions of cells expressing the gene at that level. d, e In situ hybridization with RNAscope probes confirms that Sox4 and Sox11 are expressed in both retinal progenitor cells (RPCs) and retinal ganglion cells (RGCs). Note that both genes are highly expressed in a subset of RPCs in the outside part of the retina, which presumably are the transitional RPCs. Each in situ hybridization experiment was performed three times with independent retinal sections. The scale bar is 150 µm.