This dataset introduces a new protocol called DNase-capture, a method that focuses DNase-seq analysis on selected genomic regions, resulting in a substantial increase in region-specific sequencing coverage. DNase-seq takes advantage of the preferential cutting of DNase I. DNase-capture enhances the resolution of DNase-seq by mixing a DNase-seq library with biotin-tagged bait RNA sequences that are complementary to regions of interest. In a hybridization reaction, target DNA is captured away from background DNA through streptavidin bead binding, and the captured target DNA is sequenced. Overall design: This dataset includes DNase-capture hypersensitivity data from the mES cell type. It also includes a genomic baseline.