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,
isolating whole chromatin before ChIP
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