Fig. 3.

Cell population composition and signatures of the 24 hpf hindbrain. (A) Unsupervised UMAP plot subdivides hindbrain cells into 15 clusters. Dotted lines segregate dorsal (dark violet), medial (pink) and ventral (maroon) progenitors; red arrowed lines indicate the D-V axis and the direction of neurogenesis. Below the UMAP, a schematic drawing of a representative transverse section of a 24 hpf zebrafish hindbrain at the level of the otic vesicle (DP, dorsal progenitors; MP, medial progenitors; VP, ventral progenitors; pMN, progenitors motor neurons; DN, dorsal neurogenesis; MN, medial neurogenesis; VN, ventral neurogenesis; FP, floor plate; RP, roof plate). (B) Heatmap of the top 30 genes significantly enriched in each cluster; representative gene names are shown close to each cluster. The full gene list is in Fig. S5. (C) UMAP plots showing the log normalised counts of selective representative genes. Colour intensity is proportional to the expression level of a given gene. Arrowheads indicate the relevant domain of expression; colour refers to cluster of origin. (D) Dot plot of genes with dorsoventral restricted expression in progenitors. (E) Dot plot of factors with restricted expression in differentiating progenitors. Dot size corresponds to the percentage of cells expressing the feature in each cluster, while the colour represents the average expression level. Whole-mount in situ hybridisation showing the expression pattern of atoh1a (F,F′), ascl1a (G,G′) and neurog1 (H,H′). (F-H) Dorsal view and (F′-H′) 40 µm hindbrain transverse section at the level of r4-r5/r5-r6. Scale bars: 50 µm.