Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers

We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity. Overall design: This submission contains data for two MPRA experiments. MPRA1 contains data for an inert library, a competent library, and four experimental replicates. MPRA2 contains data for an inert library and two experimental replicates. This submission also contains ATAC-seq data for hNSCs (three replicates).