Extended Data Fig. 9: Summary of results from additional mouse embryos.

a, b, Representative highest-likelihood tree analyses for additional embryos, including reconstructed trees as shown in Fig. 4a (a) and shared progenitor score heat maps as shown in Fig. 5a (b), normalized to the highest score for each embryo to account for differences in total node numbers. Here the shared progenitor score is calculated as the number of nodes that are shared between tissues, scaled by the number of tissues within each node (a single shared progenitor score is calculated as 2^{−(n − 1)}, in which n is the number of clusters present within that node). In general, the clustering of shared progenitors is recapitulated across embryos, with mesoderm and ectoderm sharing the highest relationship and either extra-embryonic ectoderm or extra-embryonic endoderm representing the most-deeply rooted and distinct outgroup, although these scores are sensitive to the number of target sites, the rate of cutting and the number of cells in the cluster. By shared progenitor, primordial germ cells (PGCs) are also frequently distant from other embryonic tissues; however, this often reflects the rarity of these cells, which restricts them to only a few branches of the tree in comparison to better-represented germ layers. The number of heterogeneous nodes from which scores are derived is included for each heat map. c, Violin plots that represent the pairwise relationship between lineage distance and transcriptional profile as shown for embryo 2 in Fig. 4c. Lineage distance is calculated using a modified Hamming distance, and transcriptional similarity by Pearson correlation. The exact dynamic range for lineage distance depends on the number of intBCs included and the cutting rate of the three-guide array. Here distances are binned into perfect (0), close (0 > x > 0.5), intermediate (0.5 ≤ x < 1), and distant (x ≥ 1) relationships for all cells that contain either three or six cut sites, depending on the embryo. As lineage distance increases, transcriptional similarity decreases, which is consistent with functional restriction over development. Red dot highlights the median, edges indicate the interquartile range, and whiskers denote the full range.