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TruSeq ChIP kit from Illumina

August 22, 2012

It appears that Illumina has finally released a TruSeq compatible kit for ChIP.  Looking at the protocol I am not very impressed.  They do a double AMPure purification like they do in the TruSeq RNA kit to get rid of the self-ligated adapter dimers and then a gel purification. From my experience there is a real risk of losing mononuclesomal DNA from native ChIP and the smaller fragments from X-linked ChIP when doing a AMPure size selection.  It makes me wonder if Bioo Scientific patented my 4 cycle PCR method to convert the Y-shaped adapters to double-stranded DNA before the gel purification step.  I’m sure Illumina’s protocol works for larger DNA fragments, say greater than 200 bp, but a lot of ChIPs have DNA fragmentation much shorter than that.  My advice for now is, unless your fragments are longer the 200 bp, stick with my protocol (best option) or use the Bioo Scientific kit.

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