Fig. 3

Characterization of enzymatically-separated syncytiotrophoblast and Hofbauer cell DNAm to closely related cell types. a Syncytiotrophoblast samples (n = 5) were projected onto principal components PC1 and PC2. Original samples used for constructing these PCs (Fig. 1a) are shown (chorionic villi: dark red, trophoblast: yellow, all others: grey). Syncytiotrophoblast (orange) cluster with the chorionic villi and trophoblast samples. b Clustering on the top 1000 variable CpGs between chorionic villi, syncytiotrophoblast, and trophoblast samples. Hierarchical clustering with Euclidean distance was used for both CpG-wise (rows) and sample-wise (columns) clustering. DNAm is shown as a range between 0 and 100%. c Density plots are shown for select differentially methylated CpGs, which were identified using limma, with a Bonferroni adjust p < 0.01, and a mean difference in DNAm > 25%. CpGs are shown along the y-axis with their locational relationship (shown in brackets) to their associated gene (left). DNA methylation is shown on the x-axis. d Clustering on the top 1000 variable CpGs between Hofbauer cells and cord blood cell types. Hierarchical clustering with Euclidean distance was used for both CpG-wise and sample-wise clustering. WBC: whole cord blood, nRBC: nucleated red blood cells, NK: natural killer cells, CD4T: CD4+ T cells, CD8T: CD8 T cells, Gran: granulocytes, Bcell: B cells, DNAm: DNA methylation