Fig. 1: Embryo-wide profiling of gene expression with spatial coordinates using Slide-seq.
From: Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
a, Schematic of the experimental workflow and data analysis. Sagittal sections of mouse embryos at E8.5, E9.0 and E9.5 were obtained for Slide-seq. The dotted lines indicate the approximate position of the embryonic sections. b,c, 3D-reconstructed E8.5 (b) and E9.0 (c) stage embryos with six cell states highlighted (brain, heart, neural tube, somites, NMPs, PSM); the caudal marker gene Cdx2 and heart tube marker gene Ttn are shown (normalized gene expression) in a vISH of the reconstructed E8.5 embryo1. Each dot corresponds to a single bead. Point of view is denoted by the eye symbol. Scale bars, 100 µm. d, 3D view of an E8.5 embryo showing the indicated cell states and anatomical features in brightfield (left) or mapped onto the E8.5 embryo1 (right). Different orientations are displayed. Scale bars, 500 µm. e, Schematic of the strategy used to identify localized gene expression in tissues. f, Heatmap of localization scores for the top 20 spatially differentially expressed genes in 3D for each analyzed tissue in the E8.5 embryo1 (see Supplementary Table 4 for the list). Top 20 genes (row z-score-normalized) in the brain are highlighted. A, anterior; LPM, lateral plate mesoderm; P, posterior; D, dorsal; V, ventral; LPM, lateral plate mesoderm; NMPs, neuromesodermal progenitors; PSM, pre-somitic mesoderm.
