I am trying to work out good approach to sequence ChIP DNA that has been amplfied with the GenomePlex Whole Genome Amplification protocol. DNA from this seems to be mostly 400-500bp. Because of the primer sequences added to the ChIP fragments (not sure how long these are - does anyone know?) it doesnt make sense to sequence these directly with Solexa.
Has anyone tried concatenation of WGA DNA followed by shearing? Are there any other approaches that are worth trying?
Has anyone tried concatenation of WGA DNA followed by shearing? Are there any other approaches that are worth trying?
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