GSM2236609: I_rep2; Zea mays; MeDIP-Seq
Genomic DNA was extracted from the samples using TaKaRa Universal Genomic DNA Extraction Kit Ver. 3.0 (DV811A) (TaKaRa, Osaka, Japan) according to the manufacturer's instructions. In total, 12 genomic DNA samples (three biological replicates at each of the four stages) were sonicated to produce DNA fragments ranging from 100 bp to 500 bp. After DNA end-repair and 3'dA-tailing using the Paired-end DNA Sample Prep Kit (Illumina, San Diego, CA, USA), the DNA samples were ligated to Illumina sequencing primer adaptors. Double-stranded DNA was denatured and immunoprecipitated using an anti-5-methycytosine monoclonal antibody (Zymo Research, Orange, CA, USA). For each biological replicate, the following procedures were performed as described (Li et al., 2010). After excising and purifying 220 bp to 320 bp bands from the gel, the products were quantified using an Agilent 2100 Analyzer (Agilent Technologies, Santa Clara, CA, USA) and qPCR qualification. Finally, ultra-high-throughput 50 bp paired-end sequencing was performed using the Illumina HiSeq 2000 (BGI, Shenzhen, China) according to the manufacturer's protocols.