How can I check the shearing efficiency working with 5000 cells per IP?
To check the efficiency of shearing in agarose gel you need an equivalent of 100.000 cells. It is not possible with lower amounts of cells. The best way is to optimize the shearing on higher amount of cells before doing ChIP on low amount of cells. If it is not possible the others known way to check the shearing efficiency are: 1. PCR-based assessment as described in Genome Biol. 2009 Feb 10;10(2):R13. by Dahl JA, Reiner AH, Collas P (supp data).
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