I have a two part question: (1) If DNA is extracted from a mammalian cell and the total quantity (yield) attained is significantly larger than what is theoretically expected considering the total number of loaded cells and the mass of DNA/cell, would it be right to consider bacterial contamination of the cell sample as possible reason, although the DNA/cell of bacteria is significantly lower than human cells? (2) If bacterial population is the reason, what would be the best solution to get rid of it?
First of all if you can afford, discard and start with fresh lot of cells. If not, once I washed the contaminated monolayer of cells with several times with concentrated Pen/strep solution and than lysed monolayer cells and replated in another plates, contamination went away
Antibiotics (penicillin):You can try adding this in one flask and others without antibiotic and compare what is happening
Did you check your cells for mycoplasma contamination? Those litte buggers can be a real pain, especially due to their small size. I would highly recommend to check for them via PCR. We had one case, where cell lines had a negative mycoplasma staining but showed very bright bands in PCR. There are already a few discussions on how to remove mycoplasma from your cell culture.
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