Extended Data Fig. 4: Enhancer accessibility of extra-embryonic lineage master regulators GATA3, GATA4 and GATA6 in human but not mouse naïve ESCs.
From: Complete human day 14 post-implantation embryo models from naive ES cells
a, ATAC-seq and RNA-seq of GATA3, GATA4 and GATA6 genes in human vs. mouse, as measured in naïve ESCs and in multiple differentiated cell types (as indicated). HENSM conditions were used for human naïve ESCs4. Known enhancers are marked in grey bars at the bottom. Putative enhancers are marked in red or green: (1) green indicates potential enhancers that are already open in naïve stem cells, (2) red indicates enhancers that are closed in naïve pluripotent stem cells, but open in at least one differentiated cell state. Putative enhancers in the approximate regions of the genes were manually selected. Open regions that overlap with promoter or exon were excluded from the analysis. RNA-seq of the indicated genes in naïve ESCs are shown. b, immunofluorescence images of HENSM ESCs cultured for 3 days in N2B27 basal medium on Matrigel-coated palates. OCT4 marks pluripotent cells (red); VIM, FOXF1, and BST2 mark the ExEM-like cells (all in cyan); SOX17 and GATA6 mark PrE- and PrE/ExEm-like cells, respectively (yellow). GATA3 marks trophoblast-like cells (magenta), nuclei (DAPI, white). Scale bar, 200 µm.
