Whole genome DNA methylation profiling of D2 medium spiny neurons in mouse nucleus accumbens using two independent library preparation methods

We isolated genomic DNA from adult male mouse nucleus accumbens (NAc) D2 medium spiny neurons (D2-MSN) by fluorescence-activated cell sorting. We performed the whole genome methylation profiling using two independent library preparation methods, namely the sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq) of Swift biosciences and the enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq) from New England Biolabs, on two identical samples. We mapped about 400 million paired-end reads to the mouse genome (build mm10) and assessed measures of each methylome by two methods. This study provided a side-by-side comparison of two independent whole genome profiling methods for low-input neuronal samples. Whole genome DNA methylation profiling of NAc D2-MSN of adult male C57BL/6J mice.