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All ctDNA markers were amplified with NEB Taq using the buffer supplied by the manufacturer (NEB co., Japan).
The amplification was carried out under the following conditions: 98°C for 3 min, 35 cycles of 98°C for 10 sec, 64°C for 30 sec, and then 72°C for 5 min, followed by 72°C for 5 min as an extension step with iProof Taq polymerase using the buffer supplied (Bio-Rad Co., USA).
The supernatant was diluted 1 5 using the buffer supplied with the assay kit and TXB2 determined according to the manufacturer's instructions (Cambridge Bioscience).
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RNAs were then phosphorylated using T4 PNK NEBB) in the buffer supplied by the manufacturer for 1.5 hr at 37°C.
Finally, the phosphopeptides were eluted twice from the TiO2 Phosphobind Resin using the Elution Buffer supplied in the kit.
The PCR step was performed using Advantage II polymerase (Clontech) with the buffer supplied by the manufacturer, 200 μM dNTPs, and 200 nM of each primer using the following program: 95°C (1 min); 35 cycles of 95°C (30 s), 55°C (30 s) and 68°C (4 min); and final extension at 68°C (3 min).
The second primer pair consisted of the upstream primer 3'andCTTTTCCTCCAACCTGT5' andownstreamam primer: 3'GGAACTaqGCAAAGGTGAGC5', Taq polymerase (Promega) was used at 1 U/μl in the buffer supplied by the manufacturer with 5 mM dNTP and 25 mM MgCl2.
For the 20 Kb library, the ligation reactions were pooled, and the 8 kb and 20 kb libraries were cleaned up using 0.4 × volumes of AMPure XP beads according to the manufacturer's instructions, with the exception that only a single wash was carried out using the wash buffer supplied with the kit.
Long-range PCRs were done using DyNazyme Ext DNA polymerase and the buffer supplied with the polymerase (Finnzymes OY, Espoo Finland).
Briefly, treated cells were collected using the lysis buffer supplied in the kit.
Standard and real-time Q-PCR was carried out with a Bio-Rad iCycler using Amplitaq Gold Applied Biosystemss) and the buffers supplied and using GMOdetect master mix (Diagenode) or supermix (Bio-Rad), respectively.
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