title: GSM2481294: wt 2 DAI rep1; Arabidopsis thaliana; Bisulfite-Seq
library_construction_protocol: DNA was extracted from dry and germinating seeds using modified CTAB method (Piskurewicz et al., Methods Mol Biol 2011). One micrograms of genomic DNA was sonicated to 200 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using SPRI beads. Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using KAPA HIFI Uracil+ (KAPA Biosystems, Wilmington, MA) using the following PCR conditions (2 minutes at 95C, 6 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).
identifiers.namespace: GEO
identifiers.id: GSM2481294