You shouldn't be able to tell how much genomic DNA is present just by a single Ct value because this will be derived from cDNA and genomic DNA with the same sequence. But you can do a control without reverse transcriptase, see what Ct value you get, and should be able to assume this is due to genomic DNA in the sample. 

Hi,

It largely depends on whether you are doing on a prokaryotic or eukaryotic system. If prokaryotic then its not possible. but if you are working with eukaryotic system then just find out whether your primer spans a intron.if so you should see two picks in the melt curve analysis for gDNA contamination.

Hi Again mohammed

Yes as mentioned By Jeffrey if you set up a 'minus RT' control then the only DNA in your reaction - apart from your primers - will be genomic DNA and so a melt curve peak in that control will indicate gemomic amplification (or alternatively primer dimers but bands in a melt curve from a 'no template' control will indicate and distinguish the latter from the fomer)

Take a look at that stratagene guide I sent you by e mail

To circumvent complications linked to genomic contamination you can  design intron spanning (exon junction) primers, as indicated by Md, and a Genbank program called primer BLAST is a useful program to design such primers:

http://www.ncbi.nlm.nih.gov/tools/primer-blast/

These primers by definition will only bind across contiguous exon exon junctions and therefore specifically target mRMA, not gDNA

Alternatively, you can digest away your genomic DNA and to ensure complete digestion of your genomic DNA without concomitant breakdown of RNA (this is a common problem with purified DNAse I solutions) the best enzyme on the market without a doubt is Turbo rDNAse I from Ambion/ABI lifesciences: This consists of just the ORF of DNAse I and thus avoids complications you nearly always encounter with pufified enzyme which despite purification can contain residual levels of RNAse and this breakdown ifor such enzymes is further exacerbated by heat inactivation of the enzyme in a process called divalent cation heat induced hydrolysis

Consequently, using the recombinant (turbo) enxyme from Ambion/ABI you can agressively digest away all of you rgenomic DNA and incur no degradation of your RNA what so ever (I have verified this with 1000s of samples using Agilent biochips). I should also add that I do not work for Ambion !!! Find attached a protocol I have optimised for this rDNase

Mohammed, as before I will post you this info by e mial because of your internet restrictions  

https://www.dropbox.com/sh/af4pcutdymydyfp/AACQ_dqDB9W_h8faArrVknlOa?dl=0

Hi Laurence,

Thanks for sharing your expertise on recognizing gDNA contamination in RNA samples. It is really helpful.