Fig. 5: Slide-seq profiling of Tbx6 KO embryos.

a, Transverse section of DAPI stained embryos (top) and spatial plot (bottom) showing the annotated tissue morphologies (somites, neural tube) and corresponding cell states in E9.5 WT and KO embryo. The KO experiment was independently performed five times in total with n > 5 embryos per experiment, and consistently yielded the same phenotype. The Slide-seq experiment was performed on one representative transversal section for WT and two for KO embryos. b, Spatial grid map showing the organization of neural tube 1, 2 and somitic cells in WT and Tbx6 KO embryos. c, UMAP showing the projection of cells assigned to the indicated clusters on the trunk trajectory (Fig. 3c), with the size of the dots representing the degree of uncertainty of mapping to the respective position. d, Dot plot showing the expression of the indicated genes in the three clusters (dot size is percentage of cells per cluster; color is cluster average normalized expression). e, RNA–FISH of the indicated genes in a transversal section of an E9.5 WT and KO embryos. The dotted lines in the schematic denote the AP position within the trunk from which sections were obtained. A representative section from WT and KO embryos at E9.5 is shown. The expression pattern was verified in two of the KO experiments with n > 3 embryos per experiment. Scale bars, 50 µm. f, Schematic showing the transcriptional identity and patterning characteristic of the ectopic neural tubes that arise in the absence of Tbx6 expression, highlighting their conflicting transcriptional identity.