Extended Data Fig. 9: scRNA-seq allows for high-resolution discrimination of cell types and their transcriptional changes due to overexpression of Ikzf2.

a, Custom annotation strategy with theoretical reads mapping to unambiguous regions of the various custom viral loci, as well as those regions that get discarded because of endogenous sequence similarity (that is, ambiguous reads). b, Violin plots of the overall scRNA-seq detection metrics, including number of unique molecules detected in each of the major cell type cluster identified (low Anc80-Ikzf2 expressing IHCs: viral Ikzf2 (vIk)⁻ IHCs n = 34; low Anc80-Ikzf2 expressing OHCs: vIk⁻ OHCs n = 132; high Anc80-Ikzf2 expressing IHCs: vIk⁺ IHCs n = 40; high Anc80-Ikzf2 expressing OHCs: vIk⁺ OHCs n = 140; and non-HCs: n = 219). c, FeaturePlots with red showing higher expression across all profiled cells, including cells identified as non-hair cells. Expression from loci captured with custom annotation shown to support cluster identification. A final labelled t-SNE plot shows all cells profiled clustered by predicted cell type. Misc, cells from all miscellaneous clusters with fewer than 5 cells; NSC, non-sensory epithelial cell; SC, organ of Corti supporting cell. Other clusters are defined by the highest differentially expressed marker gene. d, Pearson correlation scatter plots for selected genes within all profiled hair cells, hair cells from the Anc80-eGFP sample, or IHCs from the Anc80-Ikzf2 sample. e, A Pearson correlation heat map of all hair cells detected showing overall transcriptional similarities between the non-transduced IHCs and OHCs, along with the Anc80-Ikzf2-transduced IHCs and OHCs.