What are the benefits of Sonication vs Enzymatic digestion (or vice versa) for ChIP and ChIP seq?
We are planning to send Prostate cancer cell line samples for ChIP-seq, and getting chromatin fragments ~500bp after sonication (we do not have the water bath sonicator). The Core that we are sending the samples suggested we use enzymatic digestion to get proper chromatin fragmentation (100-300bp) for better results.
I am personally a fan of sonication. I have used probe sonicators and had good results. The issue I have with enzymatic digestion is that they cut at a specific motif which the location of these can be biased throughout the genome. Sonication is a largely unbiased way of fragmentation. That is why I would always suggest using sonication rather than enzymatic means.
Here is also a link to a page that goes over the options in detail:
https://www.activemotif.com/blog-sonication-guide
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