Figure 3: Type I SGNs exhibit both broad and subtype-specific tonotopic differences.
(A) Molecular heterogeneity exists along the tonotopic axis of the cochlea. Projection of single cell transcriptomes onto principal component analysis (PCA) space shows that PC2 reflects differences among the A, B, C subtypes while PC5 captures heterogeneity that corresponds to tonotopic origin. (B) Violin plots illustrate examples of genes that show either differential or uniform expression across the three tonotopic regions. Dunn’s test was used to assess significance for each possible comparison, as indicated by colored dots next to p values. See Keys. (C-D) Regional differences in expression of Kcns3 and Hcrtr2 were confirmed by RNAscope of P25 tissue sections (C), quantified in D. (E) Further analyses of scRNA-seq data revealed that some genes exhibit regional variation in a subtype-specific manner. Trends for all SGNs are shown in grey solid lines and for Ia (green), Ib (purple) and Ic (blue) SGNs in dashed lines. Error bars represent SEM. Pairs of dots indicate p values for comparisons across tonotopic regions by Tukey’s HSD test if the data were normally distributed and Dunn’s test otherwise. P values are reported only for statistically significant differences. (F) SGN subtypes are present in all regions of the cochlea, as revealed by tSNE plots showing the anatomic origin of cells (apex, middle, base) in each cluster. However, the proportions differ in the basal turn of the cochlea compared to the apex and the middle (G). Scale bars: 10 μm (C). See also Fig. S4.