Originally posted by TonyBrooks
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Since SYBR green qPCR relies on an average construct size to determine concentration, having even 10% (by mass) of your library as adapter dimer can really through your clustering off.
Oh, also we noticed that ethidium bromide seemed to wreck picogreen fluorimetry entirely and appeared to throw off qPCR as well. We frequently do a Pippin prep size selection on libraries, so this is an issue for us.
Finally, you are aware that something about the TruSeq library method causes them to out "perform" other libraries as far as clusters/pmol of library added, since you mention this above. Possibly the extra magic comes some modification to the enrichment PCR primers?
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Phillip
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