Genomic DNA from HCT116 and HCT116-TOP3B-KO cells treated with DMSO or NSC690634 (100 µM, 4 h) was extracted using the DNA–RNA immunoprecipitation sequencing (DRIP) protocol as described previously (29 (link)). Briefly, cells were lysed in TE buffer containing SDS and proteinase K (at 37 °C overnight) before being extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and ethanol precipitated. Genomic DNA was resuspended in TE buffer and digested using a cocktail of restriction enzymes (HindIII, SspI, EcoRI, BsrGI, and Xbal; 30 U each), treated with RNase A (10 µg/mL) and shortcut RNase III (2 units, New England Biolabs) before purification again with phenol/chloroform/isoamyl alcohol (25:24:1). For control samples, 10 µg of genomic DNA was treated with 20 U of RNase H at 37 °C for 3 h. The resulting genomic DNA samples were spotted on nitrocellulose 0.45-μm membranes (Bio-Rad Laboratories, CAT#: 1620115), cross-linked and blocked with PBS-Tween (0.1%) buffer containing 5% nonfat milk. The membrane was probed with mouse S9.6 antibody (1:500 dilution, at 4 °C overnight) and developed using standard enhanced chemiluminescence techniques. The same samples probed with anti-dsDNA antibodies served as loading controls.