NextSeq 500 paired end sequencing; EM-Seq for NAM lines with 2 replicates
Plants were cut off  ~1 mm above the shoot apical meristem, the first leaf and coleoptile removed, and the inner leaf tissue collected and flash frozen in liquid nitrogen. The second leaf at this stage was ~3 cm in length.  Plants were grown under growth lights with 16-hour day length at ~23 °C and harvested between five and seven days after planting.  The flash frozen leaf samples were ground to powder in liquid nitrogen and DNA was isolated using the IBI Scientific Genomic DNA Mini Kit (Plant), catalog number IB47231, following the manufacturers protocol.  DNA methylome sequencing libraries were prepared from the second leaves of 5 to 9 plants (at a stage before the unfurling of the first leaves) using the NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs #E7120S).