title: smm-seq of GM12878: BPDE treated rep 1
design: GM12878 cells were grown in RPMI medium (company) supplemented with 15% FBS, 4 mM glutamine, 100 units/mL penicillin, and 0.25 mg/mL streptomycin. GM12878 cells were cultured in T25 flasks with 5 mL of media containing either 0.125 M BPDE, or DMSO, over a total of 12 passages. Cells were counted every two days, and once they completed at least 1.5 replication cycles, they were split into new flasks at a concentration of 300,000 cells/mL. BPDE was freshly dissolved in media to the desired concentration from a 1 mM BPDE stock solution in DMSO for each passage. Genomic DNA from GM12878 cells prior to treatment, DMSO-treated cells (2 replicates), and 0.125 M BPDE-treated cells (2 replicates) at the 2-week timepoint (~12 replication cycles) was extracted using DNeasy Blood & Tissue kit  (69504, Qiagen, Hilden, Germany). Genomic DNA was fragmented by restriction enzymes. P5_HP6N hairpin adapter was ligated to the fragments. Samples were diluted based on molar concentration, and 1 uL of the sample was used as a template in pulse-RCA recation. The product of the reaction was purified and then PCR-amplified.