For those doing ChIP of transcription factor binding sites from animal cells/tissue, how important is the strain of the animal?
If I wanted to ChIP material from a Sprague-Dawley rat then sequence the fragments obtained by ChIP-Seq, I would need to map the sequenced fragments back to the Norway rat genome (same species, different strain). Is this likely to give me problems because of small sequence differences in the regulatory regions between strains?
Has anyone had any difficult/experience with this sort of thing?
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