isolating whole chromatin before ChIP - (Dec/07/2012 )

Dear all,

I am performing ChIPseq on overexpressed TFs in Drosophila wing discs. After x-linking (1% FA, 10 min) I have the problem that a two step lysis does not work anymore. Basically I am only disrupting the wing discs and lysing the cells during sonication. One of my presumed problems is now, that there might be a lot of unbound (cytosolic) TF, which I precipitate and I want to decrease this precipitation of "useless" TF. Therefore I thought to precipitate/isolate the whole chromatin before I do the ChIP. Does anyone know a good strategy how to do this? Would using spermidine do the job?

Thanks for your help,
Claudia

You may try the method described in this paper to isolation chromatin fraction from fly http://www.nature.com/nature/journal/v480/n7377/full/nature10492.html