Is that possible to get library ~200 from Chip DNA ~500

[amesapple]

Hello,

We only have a probe sonicator so my chip fragments are peaked around 500bp, ranging from 200~1000bp. The facility guy told me that he would first align the adaptors, then do the PCR (18 cycles), then do the size selection (about 200bp) from gel. My question is that if my DNA fragment centered ~500bp, there must be only a tiny fraction sizing ~100bp which can be later select from the gel. Am I right? The majority of my chip DNA would be discarded. Will this introduce bias?

Thanks a lot! Really do not want to waste my boss' money

[hon]

I wonder if it is possible to just sonicate the ChIP DNA to bring it down to around 300bp and then make the library. Recently I have this issue too, majority is on 600pb, which I don't think is good for sequencing after making library and cut the gel at 200bp. I am just trying to figure out a condition see if I can just sonicate the ChIP DNA few more cycles to bring down the size.

[amesapple]

Hi Hon,

Thank you so much for your reply. I actually figured out the problem. I found a bioruptor recently in another building. I was so happy to say that my sonication fragments are now centered around 250bp. I would make the library from 200-350bp after adaptor ligation.
So, find a bioruptor!