I need to fragment many samples of FFPE DNA of varying quality and size. Is there a uniform method of fragmentation that I can use for all of the samples? We normally use enzymatic fragmentation or mechanical shearing via Covaris but this process works best when the samples are of similar quality/size.
Thanks for any advice!
You can use mechanical shearing in a sonicating water bath. You then run out some of your sample on a gel with a ladder to see if your pieces are mostly at a size you want. Then you run out all of your sample on a gel, cut out the region of the gel with the size fragments you want, and do a gel extraction to get your DNA fragments.
Hi
You may also use ultracentrifugation to separate fragments of different size range
Hello,
You can have a look at eth Bioruptor which has been validated for FFPE derived DNA shearing. Please feel to contact me for any technical question regarding this protocol https://www.diagenode.com/files/application_notes/AN-FFPE-07_2017.pdf
Irina
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