PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA. For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier's instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier's instruction.
GEO Accession
GSM3024612