Extended Data Fig. 9. Neural tube dorsoventral patterning.

a. Heatmap showing the top 160 genes with gene expression regionalization in one of the eight generated bins along the dorsoventral axis (genes filtered by FDR < 0.01 and logFC>0.05 then ranked by FDR). A selected set of previously known genes associated with dorsoventral patterning (black) are highlighted on the right. Specific structures along the axis are highlighted at the bottom of the heatmap. Genes are row z-score normalized and listed in Supplementary Table 7. b. Heatmap showing column scaled z-score of Pearson correlation coefficients comparing the Slide-seq dorsoventral bins and the identified clusters from a neural tube single-cell reference²⁶. RP, roof plate; dp, dorsal progenitors; pMN, motor neuron progenitors; FP, floor plate. c. Heatmap showing an extended subset of the genes that display gene expression regionalization in one of the eight generated bins along the dorsoventral axis (genes filtered by FDR < 0.01 and logFC>0.05 then ranked by FDR). Specific structures along the axis are highlighted at the bottom of the heatmap. Genes are row z-score normalized and listed in Supplementary Table 7. d. Pie chart displaying differentially expressed genes along the dorsoventral axis divided by cellular and molecular function. Genes are listed in Supplementary Table 7. e. Schematic (top panel) and spatial gene expression plots of the known neural tube patterning genes in array E9.5_2. Each dot denotes a bead. The color scale depicts normalized gene expression. D, dorsal; V, ventral; A, anterior; P, posterior. f. RNA-FISH and Slide-seq quantifications for each profiled gene from Fig. 4e. Genes are bin z-score normalized (magenta: RNA-FISH; orange: Slide-seq). D, dorsal; V, ventral.