Hello,

I'm trying to quantify the copy number of the multicopy 18S gene in the HEK-293T genome using qPCR. However, the copy number of 18S per unit of DNA is higher when sonicated DNA is used as the sample in qPCR vs. when I don't sonicate the DNA (just extract from the cells using DNeasy blood and tissue kit from Qiagen). It seems like genomic DNA sonicated to a fragment size of ~3 kB gives a copy number that is ~4x as high as unsonicated DNA. Any ideas why this happens and how to get an accurate copy number?