ChIP DNA sonication problem - got too big and too small fragments (Mar/07/2005 )
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?
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.
Hi Nick, Thank you.
I used 2% gel mistakenly. I never thought of RNA showing up, which I think, makes sense.
no problemo kawaka