Extended Data Fig. 12: Identification and validation of blood- and trophoblast-like cell sub-types in human SEMs.
From: Complete human day 14 post-implantation embryo models from naive ES cells
a, normalized expression of selected blood markers (TAL1, ERG, CD34), across cells with positive (>0) expression of CD34 or TAL1. In the dashed area 6 cells which are positive to all 3 markers can be observed. b, normalized expression of key blood marker genes (TAL1, ERG, CD34) projected on a subset of SEM UMAP clusters. c, normalized expression of key trophoblast marker genes projected on SEM UMAP. Syncytiotrophoblast (STb)-like cluster (#12) is highlighted in red. d, normalized expression of key CTb marker genes projected on SEM UMAP clusters 10 (Amnion-like) and 12 (Syncytiotrophoblast-like). Cytotrophoblast (CTb)-like cells are highlighted in red. e, expression of top 50 differentially expressed genes (two-sided Wilcoxon test p-value < 0.05, logFC > 1.06 set as threshold), upregulated in Cytotrophoblast (CTb)-like cells compared to Syncytiotrophoblast (STb)-like cells. Annotation of CTb-like cells (n = 31) and STb-like cells (n = 100) was done based on the projection of SEM UMAP on the embryonic reference map (Fig. 6e). f, representative RT-qPCR gene expression (normalized by HPRT and RPL3) measured in SEM cells generated with or without BAP(J), and HENSM as control. Cell type markers were measured as following: general Tb markers (GATA2, TFAP2C), CTb-specific markers (TEAD3, TP63, OVOL1)14, STb-specific markers (CGa, CGb, SDC1) and pluripotent marker OCT4 (used as a negative control). Bar plot based panel showing the average value of each sample (which represents average value of 3 technical replicates), error bars indicate s.d. A single representative experiment out of N=3 biological replicates performed is shown.
