GSM9125333: B T2 - 3, young leaf, WGBS screening; Solanum lycopersicum; Bisulfite-Seq
Around 100 mg of the whole plant tissue were collected, snap frozen in liquid nitrogen and stored at -80oC. Tissue samples were ground using TissueLyser II (Qiagen) with sterile RNAse-free glass beads. DNA was extracted using a QIAGEN Plant DNeasy kit as manufacture's manual. The quality of the DNA was assessed using a NanoDrop spectrophotometer and Qubit fluorometer. Bisulfite libraries were prepared from 100 ng of genomic DNA using the TruSeq Nano kit (Illumina, San Diego, CA, USA), following the manufacturer's instructions, with the following modification: after adapter ligation and clean-up, samples were treated with bisulfite using the Epitect Plus kit (Qiagen, Hilden, Germany). The thermal cycle incubation was repeated once before clean-up. DNA fragments were then amplified using the Kapa HiFi HotStart Uracil+ PCR mix in 14 cycles of PCR (Kapa Biosystems, Wilmington, MA, USA). Bisulfite libraries were sequenced on an Illumina HiSeq 3000 instrument, generating 150 bp paired-end reads.