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Old 09-03-2010, 06:08 AM   #1
niceday
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Default nextera

Has anyone used Nextera library prep for illumina? I'm looking to test but any info on biases or other data would be welcome.
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Old 09-03-2010, 07:29 AM   #2
NextGenSeq
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We tried it. If you don't have a Covaris it might be worthwhile. It is very easy and fast but it doesn't give a tight size distribution.
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Old 09-03-2010, 07:32 AM   #3
niceday
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Thanks.

We do have a covaris but it's the price. We have to charge a wet lab hourly rate. If nextera can cut 2-4 hours off library making it might be useful.
I suppose we could use an ez-gel to tighten the size range.
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Old 09-09-2010, 12:55 PM   #4
epibio
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You can control the size distribution of the library, based on the buffer used (see our blog post for Bioanalyzer traces). If you want to tighten up the size range further, you could use Ampure XP.
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Old 09-09-2010, 01:14 PM   #5
epistatic
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I would use the HMW buffer, never the LMW buffer for Illumina prep. The peak at 200 represents 135 bp of the Nextera adapters and 65 bp of insert. I have had to use the HMW buffer and do size selection. Be careful if you do Size Selection post PCR, you do not have overages to re-amplify and the standard PE PCR Primers will not work.
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Old 09-10-2010, 11:31 AM   #6
epibio
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Starting with the recommended amount of DNA for Nextera (50 ng), you should get 300-500 ng of "tagmented" DNA after 9 cycles of PCR. We have some customers who don't bother with size selection, and get good sequencing results--they find that a tight size distribution is not necessary for Illumina sequencing in their application. However, it's your choice.

Also, in response to the original point, Nextera will definitely save 2-4 hours compared to Covaris + adaptor ligation.
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