The PsychENCODE resource (19) is the central website for this paper. It organizes data hierarchically, with a base of raw data files, a middle layer of uniformly processed and easily shareable results (such as open chromatin regions and gene expression quantifications), and a top-level “cap” of an integrative, deep-learning model, based on regulatory networks and QTLs. To build the base layer, we included all adult brain data from PsychENCODE and merged these with relevant data from ENCODE, CMC, GTEx, Roadmap, and recent single-cell studies (table S1 and Fig. 1). In total, the resource contains 3810 genotype, transcriptome, chromatin, and Hi-C datasets from PsychENCODE and 1662 datasets obtained by using similar bulk assays merged from outside the consortium. Overall, the datasets from the prefrontal cortex (PFC) involve sampling from 1866 individuals. The resource also has single-cell RNA-seq data for 18,025 cells from PsychENCODE and 14,012 cells from outside sources (20). These data represent a range of psychiatric disorders, including SCZ, bipolar disorder (BPD), and autism spectrum disorder (ASD). The individual genotyping and raw next-generation sequencing of transcriptomics and epigenomics are restricted
