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The denaturing temperature was 95 °C and extension temperature was 72 °C for each step, with the annealing temperatures of 66, 64, 62, 60 and 58 °C from the first to the last step.
The uniformity of the denaturization temperature, annealing temperature, and extension temperature was 1.5°C/mm, 0.7°C/mm, and 3.1°C/mm, respectively.
Approaches to mitigate primer interaction and eliminate inhibitors were tested, including: reduction of primer concentrations especially those with preferential amplification; decrease of PCR extension temperature; increase of extension time and PCR cycles; and addition of bovine serum albumin.
The primer extension temperature for segment BTAPRNPDS13a2 was conducted at 53°C for 30 sec.
Using a 55°C extension temperature, the wild type allele yields a 291 base pair band while the exon 3 floxed allele yields a 400 base pair band.
For multiplex primer reactions the extension temperature was changed to 65°C and final extension increased to 7 min. PCR was carried out on a DNA Engine tetrad thermal cycler (M J Research, Inc.; Watertown, MA).. Multiplex primer reactions were performed for combinations of primers with matching annealing temperatures but differing size ranges and dye labels.
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Optimal annealing-extension temperature was determined for each primer pair.
Denaturation and annealing-extension temperature were optimised for each assay to improve distinction between positive and negative droplets (Additional file 1: Table S1).
After the initial denaturation step at 95°C for 15 min, PCR reaction was cycled for 40 times with denature at 95°C for 30 s and annealing-extension temperature at 65°C for 30 s. Relative expression was calculated following the 2 -Delta Delta C(T)) method (55).
An alternative strategy of lowering the annealing/extension temperature (LT) at 56 °C was designed to attempt to decrease the heights of stutter peaks.
When using a separate primer and a linear template to form a polymerase substrate, rates were dependent on both the primer melting temperature (Tm) and the annealing/extension temperature.
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