After transfection of the plasmid of interest by Lipofectamine 3000 method, I harvested the cytosol at different time points, viz., 6,12,24,48,72 hours and checked the plasmid copy numbers by qPCR.

But, to my surprise, I am consistently noticing higher plasmid copy number at 12-hours post transfection, even though a media change was given 6 hours post transfection. What may be the possible reason for this?