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Fig. S1. Sequence composition analysis of the gametic DMRs. (A) Mean CpG percentage of the maternally methylated DMRs and paternally methylated DMRs as well as their 1 kb flanking regions compared with the genome (chromosome 19) and 23,021 CpG islands (Illingworth et al., 2010). Note that tentative endpoints and flanking regions were used for all three paternally methylated DMRs. Error bars indicate 95% confidence interval (CI). (B) Comparison of G+C content of the maternally methylated and paternally methylated DMRs as well as their 1 kb flanking regions. Error bars indicate 95% CI.
Fig. S2. Oligonucleotide enrichment analysis of DMRs. Mean enrichment of (A) dinucleotides, (B) trinucleotides and (C) tetranucleotides at CpG islands and the DMRs as well as their 1 kb flanking regions. Data obtained from the reverse complement sequences were included together. Oligonucleotides are shown in alphabetical order on the x-axis. Values were normalized to the mean coverage on chromosome 19. Error bars indicate 95% CI.
Fig. S3. Coverage of overlapping repetitive elements at the maternally and paternally methylated DMRs and CpG islands. (A) Mean percentage coverage of SINEs, LINEs, LTRs and tandem repeats. Error bars indicate 95% CI. (B) Box plot showing mean coverage of tandem repeats. Boxes represent the middle 50% of the samples. Grey crosses indicate sequences outside of error bars. Error bars indicate 95% CI.
Fig. S4. CpG periodicity of all maternally and paternally methylated gametic DMRs and all CpG islands. Error bars indicate 95% CI.
Fig. S5. Levels of CpG and non-CpG methylation (unconverted cytosines) in fully grown oocytes, lambda DNA and blastocysts. DNA from oocytes was mixed with unmethylated lambda DNA and bisulphite treated in duplicate (oocytes #1 and #2). Results of bisulphite sequencing are shown for representative regions of the maternally methylated DMRs of Igf2r and Kcnq1ot1 (positions of amplicons are shown at the top), and lambda DNA (lambda-A and -B). Positions of cytosines are shown at the bottom.
Fig. S6. Non-CpG methylation at the paternally methylated DMRs. Distribution and levels of CpG and non-CpG methylation at representative regions of the paternally methylated DMRs H19-I and Rasgrf1-J are shown (see Fig. 2 for the positions of the amplicons). Positions of cytosines are shown at the bottom.