We generated WGBS datasets in our previous studies for three adult brain regions (DLPFC, hippocampus and caudate nucleus). Details about study samples, data generation and data processing have been described in our previous reports14,61. Briefly, we assessed QC with FastQC. After an assessment with FastQC, we removed adapter content with TrimGalore62. We aligned trimmed reads with Arioc63 to the hg38 genome build (GRCh38.p12) and removed duplicate alignments with SAMBLASTER64. After removing duplicates, we filtered alignments with SAMtools65 (v.1.9) to include only primary alignments with a mapping quality ≥ 5. From these filtered alignments, we extracted methylation data using the Bismark methylation extractor66. After methylation extraction, we processed and combined DNA methylation proportions across samples using bsseq (v.1.18)67, an R/Bioconductor package. We locally smoothed methylation data with BSmooth using default parameters. We filtered the resulting CpG data to remove (1) CpGs within the blacklist regions and (2) CpGs with coverage < 3.
