Extended Data Fig. 10: Expression characteristics of extra-embryonic and embryonic endoderm.

a, Violin plots that represent the pairwise scRNA-seq Pearson correlation coefficients for within- or across-group comparisons according to lineage (X, extra-embryonic; E, embryonic) and cluster assignment (light blue, gut endoderm; dark blue, visceral endoderm). Within-group comparisons for cells with the same lineage and transcriptional cluster identity are shown on the left, and across-group comparisons are presented on the right. Notably, extra-embryonic cells with gut-endoderm identities show higher pairwise correlations to embryonic cells with gut-endoderm identities (column 4) than they do to visceral-endoderm cells, with which they share a closer lineage relationship (column 5). Red dot highlights the median, edges indicate the interquartile range, and whiskers denote the full range. n, number of pairwise comparisons between cells in embryo 2. b, t-SNE plots of scRNA-seq data for embryo 2, with gut-endoderm cells highlighted. Endoderm cells segregate from the rest of the embryo, and cannot be distinguished by embryonic (light blue) or extra-embryonic (dark blue) origin. n, number of cells for embryo 2. Cells of ambiguous origin are not included in the two right-most plots. c, Expression box plots for the extra-embryonic markers Trap1a and Rhox5 from an independent scRNA-seq survey of E8.25 embryos (data and annotations taken from a previous study⁹). Both genes are heterogeneously present in cells identified as mid- and hindgut but uniformly present in canonical extra-embryonic tissues, which is consistent with the presence of a subpopulation of cells of extra-embryonic origin that resides within this otherwise-embryonic cluster. Red lines highlight the median, edges indicate the interquartile range, and whiskers denote the Tukey fence. Outliers were removed for clarity.