Fig. 1

Genome-wide characterization of placental cell DNA methylation. a Principal components analysis (PCA) was applied to all samples and CpGs. Samples are projected onto axes PC1 and PC2 which account for 41% and 23% total variance, respectively. b Results from the differential methylation analysis using the R package limma are shown here. DMCs, defined as those tests passing a Bonferroni-adjust p-value < 0.01, and a difference in group means > 0.25, were divided into less methylated and more methylated compared to all other cell types. c Enrichment analysis of term cell-specific DMCs was carried out on genomic elements using a chi-squared test and a Bonferroni-adjusted p-value < 0.01. The expected (background) frequency, which is the percentage of total tested CpGs in each genomic element, is shown as a black line. d Average term placental cell-specific DNA methylation across TFAP2C transcripts on chromosome 6, and e INHBA transcripts on chromosome 7. Differentially methylated regions (defined as regions with a high density of differentially methylated CpGs), are highlighted with a grey background. Y axis ranges from 0 to 100% DNA methylation