Extended Data Fig. 8: Correlation between key TF expression and up- or downregulation of putative targets of regulation.

a, UMAP visualization of coembedded cells from cell states including anterior primitive streak, definitive endoderm, gut, and notochord (mouse E7.25 → E7.5) colored by cell type (left), Rfx3 gene expression (middle) or RFX3 motif score (right), respectively. The RFX3 motif score for each cell was calculated by averaging the gene expression of 135 key genes for notochord emergence bearing this motif in their core promoters, and then subtracting the mean expression of a reference set of randomly sampled genes, using the score_genes function of Scanpy¹⁰¹. b, Positional bias of RFX3 binding motif along the core promoters of key genes for notochord emergence (right panel), an expanded region for key genes for notochord emergence (left top panel), or an expanded region for background (left bottom panel). The y-axes indicate the % of key genes or background genes with the RFX3 motif with 10 bp bins. c, The motif logo of the top de novo motif for notochord emergence and its two best alignments in the known motif database. d, UMAP visualization of coembedded cells from cell states including primitive streak and nascent mesoderm (mouse E6.5 → E7.25) colored by cell types (left), Snai1 gene expression (middle) or SNAIL1 motif score (right), respectively. The SNAIL1 motif score was calculated as in panel a, based on 21 key genes for nascent mesoderm emergence bearing this motif in their core promoters. e, Positional bias of SNAI1 binding motif along the core promoters of key genes for nascent mesoderm emergence (right panel), an expanded region for key genes for nascent mesoderm emergence (left top panel), or an expanded region for background (left bottom panel). The y-axes indicate the % of key genes or background genes with the SNAIL1 motif with 10 bp bins. f, The known motif logo of SNAIL1.