To identify the genomic elements exhibiting transcriptional activities specific to the brain, we took a conservative approach and used the standardized and established ENCODE pipeline to uniformly process RNA-seq data from PsychENCODE, GTEx, and Roadmap (figs. S2 and S3). This consistency makes our expression data and subsequent results (including eQTLs and single-cell analyses) comparable with previous work. Using these data, we identified noncoding regions of transcription and sets of differentially expressed and coexpressed genes (21, 22).
