To annotate brain-active enhancers, we used chromatin modification data from the reference brain, supplemented by deoxyribonuclease sequencing (DNase-seq) and ChIP-seq data from Roadmap PFC samples. All data were processed by standard ENCODE ChIP-seq pipelines to ensure maximal compatibility of our results (fig. S22). Consistent with ENCODE, we define active enhancers as open chromatin regions enriched in H3K27ac (histone H3 acetylation at lysine 27) and depleted in H3K4me3 (histone H3 trimethylation at lysine 4) (Fig. 3A and fig. S23) (21). Overall, we annotated a reference set of 79,056 enhancers in the PFC. [We also provide a filtered subset (21).]
