Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577354/

As you guys know, yesterday I performed quite a few sonications and I started looking (again, as I do often) at papers that indicate the optimal size for sonicated DNA.

I found this paper. And it makes sense. It basically points out that with more sonications (~200bp) you increase the fold enrichment of your target by reducing the background or non-specific binding. But, you'll ip less (and probably purify less because the %efficiency we get back from the kits goes down with smaller fragments).

Happy ChIP'in!