The fragmentation strategy is shown for (A) conventional ChIP-seq, (B) ChIP-exo and (C) high-resolution X-ChIP-seq. In high-resolution X-ChIP-seq, MNase generates minimally protected DNA fragments that are represented by the lengths of the extracted DNA fragments, which can be obtained by paired-end sequencing. By using an AMpure size selection, it is possible to enrich for these short fragments and increase the cost-effectiveness of the technique. In contrast, conventional ChIP and ChIP-exo are designed for single-end sequencing. Furthermore, the protocols used to generate sequencing libraries for conventional ChIP-seq and ChIP-exo select against fragments below 100 bp.