Depending on how the experiment is carried out, DamID can be subject to plasmid methylation biases. Because plasmids are usually amplified in E. coli where Dam is naturally expressed, they are methylated on every GATC. In transient transfection experiments, the DNA of those plasmids is recovered along with the DNA of the transfected cells, meaning that fragments of the plasmid are amplified in the methyl PCR. Every sequence of the genome that shares homology or identity with the plasmid may thus appear to be bound by the protein of interest. In particular, this is true of the open reading frame of the protein of interest, which is present in both the plasmid and the genome. In microarray experiments, this bias can be used to ensure that the proper material was hybridized. In stable cell lines or fully transgenic animals, this bias is not observed as no plasmid DNA is recovered.