ChIP DNA sonication problem - got too big and too small fragments (Mar/07/2005 )

Hi All,

I am optimizing my ChIP sonication settings. After sonication, I did a reverse crosslink, recovered DNA by phenol extraction and ethanol precipitation. Strangely, most settings gave me a smear around 1 kb and a distinct band at 50 bp. What I expected is a smear between 200-1 kb. Should I ignore the 50 bp band?

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Hi kawaka,

I was wondering what percentage gel you are using, if it is a high percentage I suspect the band you are seeing at 50bp is tRNA or RNA contamination, I think with RNAse this band will dissappear.

Cheers

Nick

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Hi Nick, Thank you.

I used 2% gel mistakenly. I never thought of RNA showing up, which I think, makes sense.

K

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no problemo kawaka

Nick

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