So, you're doing RT-PCR, but looking at the product on a gel as a quality step and you see a product of the appropriate size in your -RT control. Do your primers span large introns? It's quite possible your DNAse digestion is incomplete. I personally like the ValidPrime method, which lets you assess the degree of gDNA contamination and correct for it. Could be interesting for you: http://www.tataa.com...pcr/validprime/
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