I have no answer but an advice: Avoid using kits as much as possible. Use of kits is equivalent of eating in McDonald's. Kit producers never provide details on kit components leaving you in the dark. Good labs never use kits in complex experiments.

It makes no sense. Where is your starting chromatin ?

Hi,

The band you see in non-purified samples must be RNA (perhaps tRNA), and your chromatin would be too faint to visualise (in the presence of so strong signals from RNA).

I recommend to treat your samples with RNase before running the gel, if you still have some left.

Play with sonication cycles and do not decrosslink more than 4 hrs. Perform RNase A treatment and stained your gel after separation.

Shin-Ichiro Hiraga I typically RNase treat before starting the reverse cross-linking step. I will attempt your suggestion and see if that changes the results.

Joseph Papamatheakis I did not run the starting chromatin because it was my understanding that it is not possible to discern useful information about the efficiency of shearing without reverse cross-linking. Do you have perspective on why it would be worth doing otherwise?

By not doing this you miss the most important information which is there chromatin at all? If the band is indeed RNA ( after your RNAse treatrment? ) where is the DNA? Especially when using a kit for the first time is good have material available from all the steps.

I just want to update this in case anyone has this question in the future; I contacted Diagenode and this effect is due to a proprietary component(s) in the elution buffer, but assured me was not due to nucleotides. I proceeded with my experiments and was able to successfully ChIP using this kit. Good luck!

The band noes not look like a nucleic acid. Ethidium bromide also stains Protein-SDS complexes, so the band could be Proteinase K + SDS (there is probably lots of it in the kit buffer). I agree with Shin-Ichiro - you do not see your sheared chromatin in these samples because of relatively low concentration.