MethylC-Seq of endosperm of maize B73
Genomic DNA (10 μg) was extracted from the embryo and endosperm using the DNeasy Mini Kit (Qiagen). The DNA was fragmented by sonication to 280-350 nt with a Bioruptor (Diagenode). The DNA was end-repaired using a mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 PNK (Enzymatics), and a 3’ overhang A was added using the Klenow exo- enzyme (Enzymatics). The resultant fragments were ligated with the Illumina methylation adapters by DNA T4 ligase (Enzymatics) according to the Illumina protocol. Adapter-linked DNA fragments were bisulfated using the EZ DNA Methylation Kit (Zymo), as per the manufacturer’s protocol. The treated DNA was amplified by PCR for 11 cycles. The DNA fragments were purified, quantified and then sequenced for 100 cycles using the Illumina protocol.