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ChIP-Chip vs. ChIP-Seq


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#1 jhb80

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Posted 27 March 2010 - 04:48 AM

Hi all,

I was wondering if / what the essential pros and cons (apart from the price...) between ChIP-on-Chip and ChIP-Seq are, respectively? I guess the resolution will be different, but when using sonicated chromatin, does this actually really factor in that much? Are there any other pitfalls (e.g. quantitative aspects)?

Really interested in hearing your thoughts...

Cheers,

Jan

#2 KPDE

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Posted 27 March 2010 - 10:01 AM

Hi all,

I was wondering if / what the essential pros and cons (apart from the price...) between ChIP-on-Chip and ChIP-Seq are, respectively? I guess the resolution will be different, but when using sonicated chromatin, does this actually really factor in that much? Are there any other pitfalls (e.g. quantitative aspects)?

Really interested in hearing your thoughts...

Cheers,

Jan


One benefit of ChIP-Seq is the ability to parse binding to sequences that differ by only a few base pairs (e.g. alleles or repeat sequences that have one or two SNPs). Still, I think a more important determinant of which to use is what kind of facilities you have available, both for running the samples and analyzing the data.




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