Efficient Genomic DNA Extraction from Cell Lines

HEK293T cells were washed with 1X PBS (Corning) and lysed overnight by shaking at 55°C with 43.5 μL of gDNA lysis buffer (100 mM Tris-HCl at pH 8, 200 mM NaCl, 5 mM EDTA, 0.05% SDS) supplemented with 5.25 μL of 20 mg/ml Proteinase K (NEB) and 1.25 μL of 1M DTT (Sigma) per well for experiments in 96-well plates, or with 174 μL DNA lysis buffer, 21 μL Proteinase K, and 5 μL 1M DTT per well for experiments in 24-well plates. K562 cells were centrifuged for 5 min, media removed, and lysed overnight by shaking at 55°C with 174 μL DNA lysis buffer, 21 μL Proteinase K, and 5 μL 1M DTT per well in 24-well plates. U2OS cells and HeLa cells were washed with 1X PBS and lysed overnight shaking at 55°C with 174 μL DNA lysis buffer, 21 μL Proteinase K, and 5 μL 1M DTT per well in 24-well plates. Subsequently, gDNA was extracted from lysates using 1–2X paramagnetic beads as previously described^{5 (link)} and eluted in 45 μL of 0.1X EB buffer. DNA extraction was performed using a Biomek FX^P Laboratory Automation Workstation (Beckman Coulter).