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Old 11-18-2013, 11:56 AM   #2
Epigenomics NGS Beast
Location: New Jersey

Join Date: Oct 2010
Posts: 17
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Hi Avo,

I have been using the truseq PCR-free preps for a year now and have never run into issues with yield at the end. Assuming you are not losing a ton of material in the shear, the double sided spri cleanup should be advantageous when compared to loss associated with selection on the BluePippin (which also requires a post selection cleanup).

I have even seen low, but good results from a 100ng input prep sheared at 350bp. If you start with 1ug and run a 350bp shear, you should end up with libraries that can be easily seen on an agilent HS DNA chip. It's not the yield you would expect from a PCR generated library, but there is plenty for sequencing and the lack of PCR artifacts make it well worth the switch for most applications.

We typically get about 100ng out of the preps. That is a ton of material for sequencing, in my opinion, even though it is a ~90% loss overall.
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