GSM9698413: Human cancer cell line, genomic DNA, cultured in matrigel (3D culture); Homo sapiens; OTHER
Genomic DNA of barcoded cell population was extracted using Quick-DNA™ Miniprep Plus Kit (Zymo, D4068). Then the barcode sequences were amplified using primers containing Illumina adapters and unique sample indices: 25 μL KAPA hotstart ReadyMix, 0.75 μL forward primer (10 μM) , 0.75μL reverse primer (10 μM) , 500ng gDNA and water up to 50 μL. The reaction is incubated as below: 95 °C for 2 min, 25× (98 °C for 20 s, 65 °C for 15 s, 72 °C for 15 s), 72 °C for 2 min, hold at 4 °C. We scaled up the number of reactions so that all gDNA can be amplified. The PCR products were then pooled and purified using HiPure PCR Pure Mini Kit (Magen, D2121) and the purified product was run on the gel before gel purification to remove primer dimers.