Hello,
I am sonicating HCT116 cells for chromatin immunoprecipitation assay on Bioruptor Pico and I have problem with size of DNA fragments. It doesn’t matter how I set the instrument, if I use few short sonication 3 x times 5 second or long 10x times 30 second, when I check fragment size on the agarose gel it is look same, always it is at the bottom, around 50bp. Only different is that at the longer sonication there is visible more DNA compare to short sonication. For DNA isolation I use phenol/chloroform isolation. I’ll be glad for any advice, thanks.
Hello Ondrey,
I am senior scientist at Diagenode in charge of fragmentation projects. I will be happy to help you with chromatin prep optimization using the Bioruptor. Based in your description, it might degraded RNA and not DNA. I will be able to advise more if you share with me more detailed protocol and a typical chromatin picture; you can contact me directly via my email address [email protected]
Irina
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