a, Heat map highlighting transcription factors from the differentially expressed genes between placental villi, trophoblast organoids and placental stromal cells. b, Heat map of genes from the ELF family of transcription factors and syncytial genes, GCM1 and ERVW-1. ELF3 and ELF5 both show moderate expression levels across the organoids and placental samples, and very low or no expression in the stromal samples. ELF4 and ELF1 are similar in all samples. There is very high expression of ELF1 in placentas and organoids. Similarly, both ERVW-1 and GCM1 are expressed at higher levels in placentas and organoids in agreement with qPCR data (Fig. 3d). c, Genomic mapping of the methylation array probes to the ELF5 gene. The height of the bars indicates the methylation level from 0 (unmethylated) to 1.0 (fully methylated). d, Methylation of the ELF5 promoter shows hypomethylation in the organoid and placental samples. e, Distribution of methylcytosine across the promoters of the 10 trophoblast gatekeeper genes identified previously in mice12. The organoids (Org) and placental (Pl) samples show very similar methylation patterns across all 10 gene promoters that are distinct from the control brain (CL) and maternal blood (MB). Box plots comprise minimum: 1.5× interquartile range, bottom: first quartile, middle: median, top: third quartile, maximum: 1.5× interquartile range. *P < 0.01, Pearson’s correlation coefficient. f, Table for results in e showing Pearson’s correlation coefficient (R), number of CpG islands or probes compared and P values. g, Chord plot representing terms from the Gene Ontology analysis of upregulated genes in trophoblast organoids.