KR12 Chem-Seq of human LS180 colorectal cancer genome
Cultures were treated with 500 nM KR12 in 0.05% DMSO for 6 h before collection. After lysis, nuclei were extracted by ultracentrifugation. Genomic DNA was fragmented by sonication before NaOAc/ethanol precipitation. DNA was purified by RNase A, treated with proteinase K and subject to phenol extraction. Following end-repaired, the reaction mixtures were suspended with AMPure XP Reagent Beads, washed with ethanol and eluted in Low TE buffer before adapter ligation, nick repair and amplification with Platinum PCR SuperMix High Fidelity mix. After library preparation and emulsion PCR, sequencing proceeded on an Ion Proton sequencer (ThermoFisher). Post FASTQ acquisition, alignment to hg19 genome were performed by TMAP.