G0gDNA Control Reads (MCF7)
MCF7 breast cancer cells were obtained from ATCC and grown in Dulbecco’s         Modified Eagle medium with 10% fetal calf serum supplemented with 100 U/mL penicillin and         100 µg/mL streptomycin. Cells were synchronized in G0 by plating at 50% confluency and serum         starving for 24 hours. The proportion of cells in S-phase was determined by FACS analysis         (BD FACSCalibur). For the G0gDNA control, undigested genomic DNA from serum starved MCF7         cells (6.8% S-phase) was sonicated to a size range of 100-600 bp Illumina libraries were         prepared using the NEBNext kit (New England Biolabs) following the manufacturer’s         directions. 200-500 bp library fragments were size selected on 2% NuSieve agarose (Lonza)         and were gel purified (Qiagen). Libraries were sequenced on the Illumina HiSeq 2000         platform.