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Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.

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Are you interested in doing this in vivo or in vitro (by in vitro I mean adding the factor to naked dna and then crosslinking)? In what species? –  Bitwise Mar 9 '13 at 1:14

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If the question here is to perform an assay that only sequences from a specific set of segments of the genome, you probably could, but it would be a lot of work and you'd need a good reason to want to go through that trouble.

Not sure how you would limit the nucleotides you get back to a specific region of the genome say. The entire point of a CHP-Seq experiment is to get as unbiased a set of nucleotides read and so using specific primers designed against only a specific set of the genome would be hard.

Usually CHP experiments focus the readout they are getting by only focusing on a specific transcription factor for instance. The number of variants of short binding sequences that usually come out will easily be read by a sequencing lane. You'd have to have a strong reason not to take all the data genome wide. Generally the results for many such pulldown sequences are pretty short and frequently can't be found uniquely on the genome, esp if there are lots of binding sites for the protein to be found.

I could speculate that you might synthesize labelled primers from random segments of a cut up library coming from a chromosomal segment you cloned somehow. That again that seems like a lot of work to cut back on the data you get from the experiment without a big reason for doing this.

Using a CHP-CHP experiment that only has specific regions tiled can make do something like this - this makes the chip itself more economical, making the experiment more accessible.

Hope this helps...

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One way to increase power (if that is your goal) is to limit your mapping step: you only seek to map to a subset of the genome, e.g. promoters or transcribed regions.

I'll post a link later, but the reference is Leuleu et al. 2010 doi: 10.1093/bfgp/elq022

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