Supplementary Figure 1: Distinct establishment patterns of H3K9me3 on genes and LTRs in mouse early embryos.

a, Scatter plot shows the enrichment of H3K9me3 in union peaks for mESC samples of this study and ENCODE data. Pearson's correlation coefficient is also shown. b, Barplot shows the Pearson's correlation coefficients between the replicates of embryo H3K9me3 samples in union peaks. c, PCA analysis of H3K9me3, H3K4me3 and H3K27me3 signals in union peaks (n = 45 biologically independent samples). d, Barplots show the Pearson's correlation coefficients between H3K9me3 and other epigenetic modifications in promoter regions. e, The UCSC genome browser view of H3K9me3 and H3K27me3 signal around Hoxa Clusters of mouse gametes and early embryos. Signals represent log2-transformed ChIP / input ratio. f, Graphs show the averaged expression level of H3K9me3 writers, including Setdb1, Suv39h1, Suv39h2 and Urf1. g, Graphs show the averaged expression level of H3K9me3 erasers, including Kdm4a, Kdm4b, Kdm4c and Kdm4d. In f and g, RNA-seq has been performed 2 times for MII oocyte, morula, E5.5 Epi, E6.5 Epi and E6.5 Exe, 3 times for 8-cell and 4 times for 2-cell, 4-cell, ICM and TE. Results for each experiment are plotted as individual points with the average value indicated by the black line.