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The PCR program was followed by a final 10 min extension step at 72 °C.
The PCR condition for short targets (<300 bp) were as follows: one cycle of 10 min initial denaturation step at 95°C, 40 cycles of 30 s denaturation step at 95°C, 1 min annealing step at 55°C or 58°C (depends on probes, see the Electronic Supplementary Material Table S4) and 1 min extension step at 72°C.
The thermic profile was as follows: initial denaturing step at 95 °C for 5 min, followed by 35 cycles consisting each of 20 s denaturing at 98 °C, 20 s annealing at 56 °C and 1 min extension step at 72 °C, followed by a final extension step at 72 °C for 5 min.
All PCR protocols included a final 5 min extension step at 72°C.
The protocol was repeated for 40 cycles and included an initial 5 min enzyme activation step at 94°C and a final 10 min extension step at 72°C.
Cycling conditions consisted of: 1) 27F/1492R-a 5 min denaturation step at 94°C followed by 30 cycles of 1 min at 94°C, 1 min at 52°C and 1 min at 72°C and concluded by a 7 min extension step at 72°C; and 2) HA-F/HA-R-a 5 min denaturation step at 94°C followed by 30 cycles of 20 sec at 94°C, 20 sec at 55°C and 1 min at 72°C, concluded by a 5 min extension step at 72°C.
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All PCRs terminated with a 3-min extension step at 72 °C and refrigeration at 4 °C and immediately used for agarose electrophoresis.
The conditions for the β-actin PCR were as follows: initial 1-min denaturation step at 94°C, another 1-min denaturation step at 94°C, 1-min annealing step at 54°C, 1-min extension step at 72°C for 35 cycles, and a final 10-min extension at 72°C.
Conditions for β-actin PCR were as follows: an initial 1-min denaturation step at 94 °C; 1 min at 94 °C, a 1-min annealing step at 54 °C, and a 1-min extension step at 72 °C for 35 cycles; and a final 10-min extension at 72 °C.
Amplifications were performed in a 2720 Thermal Cycler (Applied Biosystems, Courtaboeuf, France) under the following conditions: activation for 10 min at 95°C, followed by 40 cycles of a 30-s denaturation step at 95°C, a 45-s hybridization step at 57°C and a 90-s elongation step at 72°C, with a final 7-min extension step at 72°C.
A final 7-min extension step at 72° was then performed.
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