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ChIP sonication problems - shearing dna before actually sonicating (Jun/26/2006 )


FOr some reason I am shearing DNA without using the sonicator...any ideas on why this is happening?

I use 1% final formaldehyde for 10 minutes at 37 C and add glycine to stop the reaction for 5 minutes at room temperature. After I harvest the cells, I reverse the cross-linking and phenol chloroform extract precipitate the DNA. I get about 1500bp to 200bp of DNA before actually sonicating.


ohmy.gif Maybe it's just wierd... Could it be you have an nuclease in your buffer? blink.gif


Guys...IM haveing the exact same problem....
Actually, doesnt matter how many cycles, I still see the same DNA band size in all samples.. AROUND 1KB
but the no-sinacated samples seems fine..
Any suggestions?

Can somebody send me a protocol for CHIP....that has work on T cells...


-Edwin NYU-

could what you are seeing just be carryover RNA? This is the case if you have not RNAse treated your samples.