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PCR primers for histone mod ChIP - How to find the regions (Oct/29/2009 )

I plan to do a ChIP for various histone modifications (H3ac, H3K9me3, etc) and need to design some qPCR primers for validation of my ChIP enrichment. However I don't know of any positive controls for these modifications.

I intend to subsequently use the ChIP DNA for ChIP-seq, but most groups appear to have done the sequencing first and then validate by PCR afterwards, not the other way round. Are there any resources I can use to find regions with a high chance of having a particular histone modification?

I guess one control would be to western blot the ChIP protein-DNA complexes with my original antibody, but that doesn't tell me a great deal I don't already know.

By the way, I'll be using rat cardiomyocytes, if that helps. I hope someone has an answer! Thanks.


I've designed primers for some highly expressed genes in my cell type. Hopefully they'll work!