Extended Data Fig. 6: Spatial transcriptomics revealing InterVE in E7.5 embryos.

(a) Feature importance plot generated by decision tree showing the most important genes to enable the identification of the InterVE population. (b) Heatmap representing InterVE cells and 25 genes used for spatial transcriptomics. (c) Similar pattern as in (b) is obtained when the same 25 genes are projected in a heatmap of the identified InterVE cells in the embryo section in Fig. 4d. (d) Multiple sections of E7.5 embryos showing InterVE cells (in red, probability>0.5) identified by the decision tree. The InterVE cells are present on both anterior and posterior sides of the embryo but at this stage they are found predominantly in the anterior side. Colour-code represents the probability of a cell being InterVE. (e) PAGA trajectory inference of selected clusters in Nowotschin-2019 dataset. EmVE2 (corresponding to our InterVE) connects to various gut clusters along the anterior posterior axis of the developing gut. (f) Dotplot of AVE markers in the subclustered Nowotchin-2019 dataset. Based on CAT alignment (Fig. 2c), embryonic stage (Supplementary Dataset 4) and markers shown here, EmVE0 represents AVE at E6.5, EmVE3 and EmVE4 represent AVE at E5.5. (g) Sankey diagram representing alignments in between the Now-EmVE sub-clusters. EmVE2 (equivalent to our InterVE, Fig. 2c) is aligning with EmVE0 (equivalent to our AVE) suggesting a link between InterVE and AVE. DE - definitive endoderm, VE – visceral endoderm.