Enzymatic Methylation Seq : Arabidopsis thaliana
Genomic DNA was purified with DNeasy plant mini kit (Qiagen) from 4-5 week old leaves following the manufacturers instructions. After purification of genomic DNA, genomic DNA (200 ng) was sheared by sonication using a Covaris S2 Focused Ultrasonicator for 45 sec at 4C (Duty cycle 10%; intensity 5.0; Cycles per Burst 200) in 55 l Covaris microtube AFA Fiber Snap-Cap. After sonication, end repair/dA-tailing, adaptor ligation, oxidation of 5mC and 5hmC, deamination, and library preparation were performed with NEBNext Enzymatic Methyl-seq kit (New England Biolabs) following the manufacturers instructions. Libraries were sequenced with Illumina Novaseq SP to generate paired-end 250 bp reads. Samples were prepared from two independent biological replicates.