Wednesday, August 10, 2011

RT-PCR issues?

Hi, I can't get my RT-PCR to work and it's driving me nuts! Here's the deal: I have a set of total RNA samples that I prepped, and another set of RNA samples that I received from a postdoc in my lab. Every time I do RT-PCR (I've tried 3 times now), I am able to amplify product using his samples but not mine. This is a product that I absolutely should be able to amplify from my samples. My initial thought was that my RNA must be degraded, but I ran it out on a gel next to his samples and they look great--3 tight bands and no smears. I also ran a negative control for the PCR using RNA in place of cDNA template. I got no band for the control, so I do not suspect that his samples are contaminated with genomic DNA. Can anyone suggest anything else that might be going wrong? I seriously think I'm doing the exact same thing for both sets of samples, so I have no idea what the problem could be!

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