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In the second stage of amplification, the previously generated amplicons are amplified using primers that target the common sequence at the 5′-end of the primers [15] (Fig. 3a).
The first stage of amplification performed a current-to-voltage conversion using a feedback resistor of 20 MΩ.
Fluorescence data were collected at the end of the annealing stage of amplification.
Fluorescence data were collected during the annealing stage of amplification, and data were analyzed on the MxPro qPCR software (version 3, Stratagene).
In the second stage of amplification, universal primers corresponding to the nucleotide tag sequences amplify the first stage PCR products to a detectable level.
Fluorescence data were collected during the annealing stage of amplification, and data were analyzed on the MxPro qPCR software (version 3, Agilent Technologies Inc ,Wokingham, Berkshire, UK).
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Two cascaded stages of amplification are then used to increase the pulse energy to several microjoules.
The optical signal is filtered and subjected to three stages of amplification resulting in nominally 100 mW of average power.
Each label was quality checked through all stages of amplification and preparation for hybridisation on Affymetrix 30K chicken microarrays.
PCR primer bias is thought to be caused by inhibition of amplification by self-annealing of the most abundant templates in the late stages of amplification [ 50] or as a result of differences in the amplification efficiency of templates [ 51].
Reactions were initiated with a 15 minute incubation at 95°C followed by 50 cycles of 95°C for 30 seconds, 55°C for 30 seconds, 72°C for 1 min. The primers WD_1027_R and WD_1028_R had 5'-tags of M13 forward and reverse primer sequences, respectively, to serve as anchors for the degenerate primers in later stages of amplification and were later used for sequencing.
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