Extended Data Fig. 7: Patterning of the developing brain.
From: Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
a. Spatial velocity length (left) and confidence of directionality (right) highlight regions with different dynamics. Scale bar, 200 µm. Array shown is E9.5_3. b. Combining the length and confidence measurement results in ‘low’ and ‘high’ velocity regions. Regions with ‘low’ velocity display lower length and lower directionality. Regions with ‘high’ velocity display higher length and directionality of the vector. Scale bar is 200 µm. Array shown is E9.5_3. c. Inset regions of the RNA velocity in the brain region with expression of markers defining the respective boundary regions (representative of 3 independent E9.5 arrays). Each dot corresponds to a bead. Color scale denotes normalized expression. Scale bar, 50 µm. d. Spatial plot of WNT genes at R2 (Telencephalon-diencephalon boundary – denoted arrows; representative of 3 independent E9.5 arrays). Each dot corresponds to a bead. Color scale denotes normalized expression. Scale bar, 50 µm. e. Slide-seq based schematic of the developing eye. The forebrain (dark blue) and the eye (orange) are depicted with the fraction of beads corresponding to each state (bar plot). 1499/4824 beads for the forebrain/anterior neural tube; 105/4824 beads for the eye/anterior neural tube; and 105/1499 beads for the eye/forebrain. Spatial plot showing the expression of the eye-specific marker Six6. A, anterior; R, rostral; C, caudal; D, dorsal; V, ventral. f. Spatial plots showing the expression of two newly identified eye marker genes, Cp and Vwc2 (left: whole E9.5_3 array; middle: subset of the ‘eye’; right: RNA-FISH validations for Cp and Vwc2 (magenta) and counterstained nuclei (grey) are shown for a representative embryo. n = 3 embryos/experiment, 3 independent experiments). Scalebar, 200 µm. R, rostral; C, caudal; D, dorsal; V, ventral.
