use genomic DNA or cDNA? - (Nov/07/2006 )
When you do the RNAi,will you use genomic DNA to amplify your target gene or cDNA? Which one will be better?
I only have the cDNA sequence. Is that OK?
Thanks for your time.
You mean RNA interference right? So I assume, you have transfected your cells with siRNA oligoes or shRNA vector for your gene of interest and you want to confirm whether there is any silencing. In RNA interference the mRNA transcripts of the target gene are cleaved. Therefore the silencing can be elucidated by level of mRNA(RT/Real Time PCR) or of protein (Westen blot). So you will have to do PCR taking cDNA and not genomic DNA.