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Economical ChIP-seq library construction with TruSeq Adapters

February 6, 2012

I made a library using substantially less enzyme than I have in the past. As I expected there appears to be no noticeable reduction in efficiency.  As sequencing costs plummet, the cost of library construction is becoming significant. It is pretty funny thinking about it.  This protocol was based on the original Illumina ChIP-seq protocol, which is a protocol most everyone has followed. As with most protocols, it usually comes down to some guy in a lab adding 1 μl of enzyme and/or the most enzyme that will fit into the tube. This is understandable when this hypothetical guy just wants to finish an experiment, but I don’t understand how a company selling kits couldn’t take an extra day to optimize the amount of enzyme used. That being said I am still not 100% sure the protocol with the reduced enzyme usage is as efficient. If it is less efficient the difference is pretty small, as in less than one cycle of amplification required. This newest version is here:


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