Let say that I am doing qPCR of genomic DNA with two sets of primers specific to two different promoters of gene A and gene B. If both gene A and Gene B are single copy, and my primers for A and B are specific for the A and B promoters, should quantitative real time PCR amplify the promoters A and B with the exact same kinetics (assuming a specific product with 100% efficiency?) In other words, if my Ct value for gene A is 25, should my Ct value for gene B also 25?
Or could the Ct values be different, based on the sequences of my primers?
Also, any references for the answer to this question
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qPCR and comparing copy number between different genes.
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