Genome-wide mapping of DNA damage hotspots in response to various replication stressors

Purpose: The goal of this study is to profile and identify DNA damage hotspots that are sensitive to different replication stressors. Overall design: Methods: Human lymphoblastoid cell line is treated with aphidicolin, hydroxyurea, or methyl methanesulfonate for 24 hours, and ChIP with gamma-H2AX were performed. Two independent ChIP experiments for each treated and untreated samples were carried out. ChIP DNA was then subject to Illumina sequencing using Hi-Seq 2500. Sequence reads that passed quality filters were mapped to GRCh38 using Bowtie2. Peaks were then analyzed for enrichment of repetitive sequences, CpG islands, transcription start sites, and histone marks.