Fig. 7.

Fig. 7. Identifying progenitor populations from shox2^+/+ and shox2^Δ/Δ embryos. Cell clusters that correspond to progenitors from the course-grain map were bioinformatically extracted and reanalyzed by unsupervised clustering before visualizing on UMAP coordinates. (A) Plot of progenitor populations from shox2^+/+ (magenta) and shox2^Δ/Δ (green) cells were identified using library identification barcode for each cell type. (B) Fine-grain UMAP plot shows 12 distinct cell clusters labeled from 0-11. shox2^+/+ clusters are labeled in black and shox2^Δ/Δ in red numerals. Dot plots were used to display marker gene expression. Each dot represents two values, the color of the dot represents relative gene expression levels and the size of the dot represents the percentage of cells expressing the gene. Hierarchical clustering identified related cell populations and the dendrogram represents the relationship between cell clusters. shox2^+/+ and shox2^Δ/Δ cell clusters are marked by black and red numbers, respectively. (C) Identifying otic progenitor (op) population that express inner ear marker genes (oc90, six1a, six1b, eya1 and neurog1) were used to identify wild-type otic progenitor population. Hierarchical clustering revealed otic progenitors from wild-type and mutant cells that are highlighted by a blue box. (D) Identifying rhombomere cell populations expressing different hox genes (hoxa2b, hox2a, egr2a, egr2b, hoxb1a, hox1b, hoxb3a, hoxa4a and hoxd4a). Cell clusters were subjected to hierarchical clustering to identify cells from rhombomere (r) 5, 6 and 7. Cell populations from wild-type and mutant cells that are shaded in purple, red and green. (E) Expression of otic and developing rhombomere marker genes in progenitor populations. Dendrogram displays the relationship between clusters. Otic progenitor cluster are highlighted in blue, rhombomere 5, 6 and 7 clusters are highlighted in purple, red and green box, respectively.