ChIP-PCR: Amplification in IgG negative control - (Oct/27/2011 )

Hi,

I have a basic question about PCR after ChIP.
So while trying to do this ChIP-qPCR, yes qPCR, I got difference between Ct values of my target antibody IP and IgG IP as 2, so 33 and 35.
But when I ran this product on a gel, I got bands in both target IP and IgG IP, is that normal, since I am looking at the end product of PCR cycles after 50 cycles ?

Thanks !

Short answer.......Yes, it is normal. However, a 6.66 fold difference between your specific IP and isotype IP is rather small. With that said, it really doesn't matter too much if your Fold Enrichment at your DNA region of interest is greater than your Fold Enrichment at a negative control DNA region