Supplementary Figure 3: Landscape of allelic specific H3K9me3 during early embryo development.

a, Heatmap shows the Pearson's correlation coefficients of BDF1 H3K9me3 samples and C57BL/DBA H3K9me3 samples. b, The UCSC genome browser view of allelic H3K9me3, H3K4me3, H3K27me3 and DNA methylation level near gene Etv6. Signals represent ChIP-seq RPM for histone modifications and absolute level for DNA methylation. c, Boxplots show the allelic H3K9me3 signal of different clusters in Fig. 4c. n = number of H3K9me3 domains between different groups. The center represents the median value and the upper/lower line represent 5% and 95% quantile for the boxplots. d, Bar plot show the fraction of maternally-expressed (left) and paternally-expressed (right) imprinted genes that regulated by allelic specific H3K9me3, H3K27me3 and DNA methylation. ChIP-seq for H3K9me3 has been performed 2 time for each stage except late 2-cell (3 times) and data shown represent average values. WGBS for each sample was performed once. e, Pie chart show the overlap of maternal specific H3K9me3, H3K27me3 and DNA methylation regulated imprinted genes at ICM stage. H3K27me3 ChIP-seq data for MII oocyte, sperm, late 2cell and E3.5 ICM were from public data (GSE76687).