I am currently using a bench top Sonicater at 30% amplitude for 20 cycles (15 sec on, 45 sec off). I am getting chromatin fragments around ~500bp which works for our ChIP-qPCR, but despite trying optimization, we are not getting fragments in the range of 100-300bp, that is required for ChIP-Seq.
What protocol do you use and how do you get the proper fragmentation of chromatin in your ChIP and ChIP-Seq experiments?
You do not need the fragments to be that small. You can simply do a size selection. Size selections can be done with Ampure XP beads or a BluePippin or an agarose gel. For my ChIP-seq experiments I also selected fragments from 100-450bp and had rather sharp peaks. Also I would recommend reducing the amount of sonication and then doing a size selection. I would then run a qPCR for enrichment of euchromatin vs heterochromatin to make sure there is not a bias. If you do this and have good enrichment via qPCR for your binding sites than you should be good.
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