Figure 4.

Single-cell RNA-seq (scRNA-seq) reveals the main cell types of cochlear epithelium during organoid development

(A) Overview of the scRNA-seq of cochlear organoids at different stages.

(B) The scRNA-seq datasets from P2 organoids cultured in the expansion medium were integrated with the differentiated day 5 and day 25 organoid datasets and projected onto UMAP plots. Colors denote the five main cell clusters from three different time points.

(C) Violin plots showing the expression of representative genes across the five main clusters.

(D) The proportion of cells from each cluster in the indicated stages.

(E) Heatmap showing the most highly expressed genes of the five main clusters. Each gene group’s GO enrichment analysis results are displayed to the right.

(F) Visualization showing the expression of potential marker genes for clusters 2, 4, and 5.

(G) RNA-scope analysis of ACBD7 and CCER2 mRNA expression of the P2 cochlear epithelium. HCs were stained for MYO7A. Scale bar, 50 μm.

(H) Real-time PCR analysis showed the relative expression of HC-related genes. Results were normalized to GAPDH in the same sample and then normalized to the expansion group (n = 3 independent experiments). The data are presented as means ± SEM. ^∗p < 0.05, ^∗∗p < 0.01, ^nsp ≥ 0.05 (one-way ANOVA followed by Tukey’s multiple comparisons test).