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Identification and annotation of cell types from Louvain clustering.(A) Uniform manifold approximation and projection (UMAP) plot colored by Louvain clustering showing six clusters that included rpl10-HA (RiboTag) positive and negative cells. (B) Violin plots of selected marker genes of hair cell (HC) and SC. High levels of transgene tg_rpl10_3X_HA_short transcripts were concentrated in cluster #0, 1, 3, and 4 indicating they are cells within the HC lineage. Relative lower levels of rpl10-HA transcripts were found in cluster #2 of unknown identity, and #5, which expresses a high level of a SC marker, si:dkey-205h13.2. (C) Distribution of selected marker genes in UMAP. tg_rpl10_3X_HA_short is distributed in all the clusters except cluster #2. Supporting cell markers, si:dkey-205h13.2 and klf17 positive cells are concentrated in cluster #5. Thus, clusters #2 and #5 were excluded from the reclustering. (D) UMAP plot of reclustering of #0, 1, 3, and 4 shown in (A). (E) Heatmap showing the top 30 genes expressed in each cluster after the reclustering. (F) Violin plot showing distribution of n-counts, n-genes, mitochondrial fraction, and percentage of ribosomal genes of each cluster. The lower count depth, lower transcripts, and higher fraction of mitochondrial genes in cluster #2 indicate that they are damaged HCs. High percentages of ribosomal genes in clusters #3 and #4 are features of HC precursors and nascent HCs (Lush et al., 2019).
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