I have > 60 samples to run in qRT-PCR, and I need to determine the gene expression of ~10 genes. Here is my problem, I would like to run my samples in triplicate, but I am not sure what is the best way to setup a 96-well plate. I am working with SYBR green chemistry.
Can I run one gene/plate assuming that their PCR efficiencies are similar?? I know it will be best to run my endogenous control with my target genes, but since I have many samples I am not sure what would be the best solution. Also if my PCR efficiencies are different should I try to find a better housekeeping gene or is there an algorithm that can help solve the problem.
Thank you very much for your time :)