Endogenous and exogenous chemical modifications in DNA have profound influences on genome function. We have developed a novel technology, Nick-seq, for mapping variety of DNA chemical modifications across the genomes at single-nucleotide resolution, by which we achieved quantitative profiling of single-strand breaks, phosphorothioate modifications, and oxidative DNA damage sites. This method is applicable for mapping of any DNA metabolism events that are involved in or can be converted, enzymatically or chemically, to DNA strand breaks such as DNA modifications, damages, genome replication, and chromatin structures. Overall design: 2 sample treated by different nickase were used. For each sample, there is one negative control.Then for each sample, two library prep methods were ultilized.