Extended Data Fig. 9: Cross-species analysis of primate mesoderm differentiation in vivo.

a, Alignment of EmDisc-derived postimplantation lineages in marmoset and human. Visualization based on alignment of embryo in vivo and in vitro datasets of pre- to postimplantation cynomolgus monkey²⁵, in vitro-cultured human¹², in vivo human CS7⁹, preimplantation marmoset (ref. ²⁴ and this study), and postimplantation marmoset embryo data (this study) were aligned. UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. b, UMAP plots of marmoset CS5–7 or human late CS7 lineages showing normalized log expression of marker genes from⁹. Pluripotent EmDisc (Embryonic Disc): SOX2, CDH1; Primitive Streak: CDH1, FST, TBXT; Nasc Mes (Nascent mesoderm): TBXT, CDH2, Emergent Mesoderm: OTX2, LHX1; Advanced Mesoderm: FOXF1, HAND1, BMP4, GATA6; Amnion: VTCN1, HAND1, BMP4; Endoderm subcluster also indicated by co-expression of CDH2, OTX2, GATA6. c, Unbiased clustering of gastrulation stage lineages represented in UMAP in (a) resolves 9 clusters by shared nearest neighbour clustering: Pluripotent EmDisc (Embryonic Disc), PS early (Primitive Streak early), PS late (Primitive Streak late), PS advanced (Primitive Streak advanced), Endoderm, Nasc Mes (Nascent Mesoderm), Em Mes (Emergent Mesoderm), Adv Mes (Advanced Mesoderm), PGCs (Primordial Germ Cells). d, Bifurcation of endoderm and mesoderm from the primitive streak represented in a diffusion map. Human CS7 shows an additional route from primitive streak to advanced mesoderm through emergent mesoderm. Alignment includes data plotted in (c) with amnion and PGC clusters excluded where cluster identity is given by colour. The first 2 diffusion components are shown (dim 1, dim 2). e, Diffusion maps of marmoset CS5–7 or human late CS7 lineages showing normalized log expression of marker genes for primitive streak (TBXT), endoderm (FOXA2), pan-mesoderm (SNAI2, CDH2), emergent mesoderm (OTX2) or nascent mesoderm (FOXF1). f–g, Human vs. marmoset scatterplots of primitive streak vs. nascent mesoderm (f) or nascent mesoderm vs. endoderm (g). Highlighted quadrants show human-marmoset conserved markers for each lineage, whereas white quadrants show species-specific expression patterns. Gene names for transcription factors, ligands, and extracellular matrix molecules are labelled.