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-   -   Questions regarding ChIP sonication and ChIP-Seq on heterochromatin (http://seqanswers.com/forums/showthread.php?t=66662)

aquleaf 03-03-2016 07:15 AM

Questions regarding ChIP sonication and ChIP-Seq on heterochromatin
 
Hi all. I have a problem regarding ChIP sonication. We are culturing one type of cells in two different states. One state shows active transcription (say State A), while the other one shows decreased overall transcription activity (say State B). We found that State B cells were very difficult to be sheared by sonication. The common solutions in this situation are to increase sonication power and extend the sonication treatment. However, we suspect that even though enhanced sonication might generate more small fragments, these fragments might be from chromatin with destroyed protein-DNA structure. The amount of ChIPed DNA might not increase much or even decrease. Thus, it seems that increasing the cell amount might be a good choice. But, the problem is we want to compare the binding profile differences between two states. Is that OK if we use different cell amounts in ChIP of two states of cells?

One more question. Is there anyway to perform ChIP-Seq on heterochromatin marks?

Thanks a bunch! Any help will be greatly appreciated.


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