DNA methylation seq of rat: adult male nucleus accumbens
We used the SeqCap Epi Enrichment System for target bisulfite sequencing of promoters and enhancers in the rat genome. The rat (rn4) target probes were custom designed by utilizing H3K4me1 and H3K4me3 (indicating enhancers and promoters, respectively) signals from mouse samples. A total of 53374 target probes have been designed spanning 48072248 base pairs of sequence with a mean probe size of 900 bp. Biotinylated target probes were designed for both strands of bisulfite converted genomic DNA. Bisulfite treated genomic DNA was ligated to methylated next generation sequencing (NGS) adaptors, hybridized to the biotinylated oligonucleotide probes followed by a series of washes of off-target DNA sequences and unbound DNA. The resulting isolated specific DNA then underwent PCR amplification for downstream sequencing on Illumina Hiseq 2000 sequencer. Capture and hybridization was performed by IRCM (Montreal, Canada; licensed by Roche/Nimblegen).