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Polymerase chain reaction (PCR) was performed in a thermal cycler (Applied Biosystems® Veriti®, California, USA) using a total reaction volume of 10 μl.
following the manufacturer's guidelines in 24- to 34-plex reactions in 384-well plates using a total reaction volume of 5 µl including 12.5 ng of genomic DNA.
Thereafter, qRT-PCR was performed using a total reaction volume of 20 μL, which contained 0.5 μL of diluted cDNA, 8 μM primer mix, 10.0 μL of 2× SYBR Green Mix, and 8.7 μL ddH2O.
Quantitative real-time PCR was performed using a total reaction volume of 25 μl, containing 5 μl of diluted cDNA, 12.5 μl iTaq SYBR Green Supermix with ROX BioRad Laboratoriess, Hercules, CA) and 0.03 μl of each oligonucleotide primer (250 μM).
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Assays used a total reaction volume of 20 µL incorporating 9 µl master mix with SYBR green I and 10 µM of each primer and 2 µl cDNA.
For QSD assays a 5µl aliquot was used in a total reaction volume of 25 µl using a previously described TaqMan assay [51].
For each reaction, 2.50 μl of 2× TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems, Foster City, CA), 0.25 ul of 20× SNP Genotyping Assay Mix, and 2.25 μl of genomic DNA at 10 ng/μl were used for a total reaction volume of 5 μl using 384-well plates.
To determine relative gene expression levels using quantitative Real Time PCR (qRT-PCR), 1 μl cDNA was used in a total reaction volume of 10 μl 1× SYBR® Green PCR Master Mix (Applied Biosystems) with final primer concentrations of 0.5 μM.
A similar procedure was used for the bleaching of BR where 100 mM hydroxylamine was used with a total reaction time of approximately 24 h.
qPCR experiments were conducted using MESA Blue qPCR MasterMix Plus for SYBR Assay Low ROX from Eurogentec, this 2× reaction buffer was used in a total reaction volume of 12.5 μl.
To determine relative gene expression levels using quantitative Real Time PCR (qRT-PCR), 2 μl of a 20-fold diluted solution of cDNA was used in a total reaction volume of 10 μl 1× SYBR® Green PCR Master Mix (Applied Biosystems) with final primer concentrations of 0.5 μM.
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