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I have few samples with different concentration of RNA (some have low concentration of RNA). I wonder if I can synthesis my cDNA using different amount of RNA template ( 1ug and 0.5ug) which will be used of end point PCR and RT-PCR.
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I suppose if it were quantitative qPCR you could do 0.5 ug for all samples. Since it's endpoint, and presumably not really quantitative, you can do as you please. If you're trying to be somewhat quantitative, I suppose it's better to use the same amount of RNA, and stop the PCR while it's still amplifying geometrically, before it reaches plateau, as the plateau level is initial concentration independent. The difference between 0.5 and 1 ug, 2 fold, is only one cycle so not that much is gained by using different amounts. Your RT enzyme should come with instructions on the RNA amounts it can take optimally.
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You can also ethanol precipitate the low concentration RNA sample and redissolve it in less water to make it the same amount as other samples.
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