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Old 05-02-2011, 01:36 AM   #1
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Default Large insert libraries

Has anyone managed to make mate pair libraries with an insert size of over 5kb as supported by Illumina? Is there anything different in the circularization stage?
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Old 05-02-2011, 11:28 AM   #2
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Illumina doesn't support anything but the 2-5kb protocol, currently. But one can ask nicely and they will provide a beta - it doubles the starting material and the volumes(and components) for the first end-repair and biotinylation. I have prep'd a 5kb using both ways and had a better yield to go onto the HiSeq using the 5-10kb beta protocol. Another tip is to start with quality template (dna in my case).
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Old 05-03-2011, 06:46 AM   #3
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I have heard that the Broad Institute is using 40kb fragments somehow to produce vertebrate genomes from Illumina, but I don't know any details.
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Old 05-03-2011, 10:07 AM   #4
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The Broad strategy first creates 40kb-insert fosmids by traditional cloning, which are then used to generate mate-pair libraries. Details are in the supplement of their recent ALLPATHS-LG paper (Gnerre et al, 2011 PNAS).
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