Mo17 MethylC-seq
Whole-genome bisulfite sequencing was performed adapting methods from Schmitz et al., 2011. Briefly, 14-day whole-seedling gDNA was isolated from B73 and Mo17 inbred lines planted independently from samples used in meDIP analysis. Samples were fragmented, and TruSeq methylated adapters were ligated to DNA fragments. 500ng of adapter-ligated DNA underwent bisulfite conversion using the MethylCode bisulfite conversion kit (Life technologies) per manufacturers protocol. Converted DNA was split into 4 reactions and amplified using Pfu Turbo Cx DNA Polymerase (Agilent) for four cycles and subsequently pooled. Libraries were sequenced on the HiSeq 2000 (Illumina) for 100 cycles, paired-end.