I'm genotyping about 100 clones that i have transfected with a gfp reporter plasmid (co-electroporation with a rtta cassette that has a resistance gene). The gfp does not have a resistance cassette so I am typing all of my clones for gfp. The issue is that my negatives keep coming up positive. I have switched all of my reagents, tried two different primer sets and protocols, and am extremely cautious with my equiptment.
My negatives are 1) h20 and 2) genomic mouse dna that is gfp-negative. One of the protocols I have used includes an internal control which amplifies the mouse negative but not the water.