title: GSM2559477: M82 rep1 MethylC-seq; Solanum lycopersicum; Bisulfite-Seq
library_construction_protocol: DNA from leaf (2-week-old seedlings), mature flowers or pollen was extracted with the Puregene kit (QIAgen) following manufacturer's instructions. Bisulfite library preparation was performed with a custom protocol similar to Urich et al. (2015). 1.2 µg DNA was sonicated on a Covaris E220 to a target size of 400bp and purified on XP beads (Ampure, ratio 1.8). DNA was end-repaired and A-tailed using T4 DNA polymerase and Klenow Fragment (NEB) and purified again using XP beads (ratio 1.8×). Methylated Illumina Y-shaped adapters for paired-end sequencing were ligated using Quick-Stick Ligase (Bioline). 450ng of purified (ratio 1.8×), adapter-ligated DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer's instructions. DNA was barcoded using 12 cycles of PCR amplification with KAPA HiFi HotStart Uracil+Ready Mix (Kapa Biosystems) with PE1.0 and custom index primers (courtesy of the Sanger Institute)
attributes.tag: GEO Accession
attributes.value: GSM2559477