Extended Data Fig. 8: Transcriptional dynamics in the trunk region.
From: Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
a. Spatial plot showing beads from E9.5 embryo (array E9.5_6) corresponding to the NMPs, PSM, somites and neural tube clusters (left panel) and the corresponding pseudotime values (right panel). Each dot corresponds to a bead. Cell states are highlighted in the indicated colors. Scale bar, 200 µm. b. Heatmap showing the expression of pseudotime determining genes along the somitic and neural trajectories. Genes used for the heatmap are listed in Supplementary Table 6. c. Line plot showing gene expression of selected genes along the neural and somitic trajectories. y-axis represents scaled gene expression. d. Schematic workflow of the ‘axis profiling’ tool. e. Pie chart displaying differentially expressed genes along the anteroposterior axis divided by cellular and molecular function. Genes are listed in Supplementary Table 7. f. Line plot showing the spatial distribution along the anterior-posterior axis of the Hox modules’ expression (I-VI). g. vISH for Hox genes in 3D virtual E9.0 stage embryo. Scale bar, 200 µm. D, dorsal; V, ventral; A, anterior; P, posterior.
