Extended Data Fig. 10. Tbx6-KO spatial profiling.

a. Schematic of Tbx6 gene ablation strategy. Guide RNAs target the denoted exons. UTR, untranslated region. b. Schematic showing the plane of cryosectioning for Slide-seq experiment. c. Spatial plot of all cell states in the complete WT and Tbx6-KO trunk transversal arrays. Dotted lines denote the region that was used for further analysis. Each dot corresponds to a bead. Each color represents an individual state. Scale bar, 200 µm. d. UMAP, spatial and fraction plot showing the filtered and de novo annotated cell states. e. Dot plot depicting the expression of neural tube and somitic marker genes in the somites, neural tube 1 and 2 clusters. The size of the dots represents the % of cells expressing the gene, and the color represents the cluster average normalized expression level. f. Scatter plot showing differentially expressed genes between somitic vs central tubes clusters and central vs ectopic tubes clusters (genes filtered by FDR < 0.01. Complete list of genes in Supplementary Table 9. g. RNA-FISH of Foxa2 and Pax6 in a transversal section of the neural tube in WT and Tbx6-KO embryos. The schematic represents the anteroposterior position where the transversal sections were profiled. Scale bar, 50 µm. D, dorsal; V, ventral; WT, wild type; KO, knockout.