Extended Data Fig. 9: Coembedding of 825 cell states from three species by integrating their transcriptional features.

For cell states spanning multiple time points, cells from each time point were treated separately for the purposes of this analysis. To create a transcriptional feature corresponding to each cell state (that is a pseudocell), we first averaged cell-state-specific UMI counts, normalized by the total count, multiplied by 100,000 and natural-log-transformed after adding a pseudocount. We then divided all resulting 825 pseudo-cells from the three species into four groups: the mouse single-cell group (n = 151), the mouse single-nucleus group (n = 277), the zebrafish group (n = 205), and the frog group (n = 192), and performed the anchor-based batch correction¹³. UMAP visualization shows coembedded pseudo-cells from the mouse (red), the zebrafish (blue), and the frog (green). Each circle corresponds to a pseudocell, and the numbers correspond to the cell–state labels shown below. The grey dotted curves (manually added) highlight 15 major groups, each including representatives from all three species. Cell states from the extraembryonic lineages (inner cell mass, hypoblast, parietal endoderm, extraembryonic ectoderm, visceral endoderm, embryonic visceral endoderm, and extraembryonic visceral endoderm for the mouse; blastomere, EVL, periderm, forerunner cells for the zebrafish) were excluded from this analysis. For E6.5 of mice, we only used cells from a single study². PNS: peripheral nervous system. MHB: midbrain–hindbrain boundary. Di: diencephalon. DEL: deep cell layer. EVL: enveloping layer.