Comprehensive WGBS Data Analysis

WGBS was performed using the AccelNGS Methyl-Seq DNA library kit (Swift Biosciences, #30096). The sequence was generated on Illumina HiSeq or NovaSeq instruments and reads were mapped with biscuit, as described in https://github.com/genome/analysis-workflows/blob/v1.5.0_fix_1/definitions/pipelines/bisulfite.cwl. The “metilene” algorithm was used to analyze the methylation ratios at all CpGs to identify differentially methylated regions (DMRs). Each DMR was required to span >10 CpGs, have a mean methylation difference between groups of >0.2, and a false discovery rate (FDR) <0.05. Adjacent DMRs <50 bp apart were merged, then non-canonical DMRs with standard deviation within either group of >0.1 were removed^{24 (link)}. Gene annotations (gene bodies, transcription start sites, promoters, and enhancers) are based on protein-coding genes from Ensembl release 95 and its accompanying regulatory build.