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I'm looking at automating library prep for both titanium and for GAII. Does anyone know of a good solution for this? I'm planning on setting up my own system, but would be interested if there are any products coming out to do this...
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Last edited by 454newbie; 03-08-2011, 10:28 AM. -
Illumina is supposed to be coming out with a gel-free sample prep method that should be pretty easily automated, but haven't heard any specific details... anyone else? -
Yes- I think this just uses Ampure beads in place of the gel. I'm pretty sure it should be straightforward to replace all the minelute columns with AMPure, too. automating this would be v.easy, just figured I'd see what else everyone out there is tryingLast edited by 454newbie; 03-08-2011, 10:28 AM.Comment
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Covaris E210
Hello 454newbie,
Please forgive the fact that this is my second post.
I would be happy to discuss with you how our Covaris E210 instrument would automate your library prep. http://www.covarisinc.com/e_series.htm
Please feel free to email me at [email protected] for any additional information. I can also refer you to our applications scientist for your technical questions.
Best regards,
JoonComment
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thanks. that's not the part I'm working on automating. I want to automate the process after shearing. all of the standard steps including column purifications.
Any suggestions?Last edited by 454newbie; 03-08-2011, 10:28 AM.Comment
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Yes, these can certainly replace the columns ... but these alone won't be able to replace the size selection gel will they?Originally posted by 454newbie View PostComment
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Auto Library
Ampure is suitable for small size DNA selection especially when recovery is a concern, which is within the range Illumina. For large size DNA selection, Aline bioscience's PCRclean actually works better. They are all magnetic beads based so it can be automated.
There are other 3-minute magnetic beads based technologies that can streamline the whole process to replace the column based method.
Originally posted by 454newbie View PostComment
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I heard there are a few systems coming out. however they are all very expensive to buy and to run. I think the solution is a semi-automated process so that you can change reagent at will based on price and needs. I have used DNA Normalizer for the DNA purification steps, it appears to be superior than other method. It is magnetic based and use takes three steps. One bind, one water wash, and then elute. A few minutes protocol. The method is for normalization but I found it good for DNA clean up as well. Automation can be modulized this way and copied at each step. Size selection has to be done differently though.
Originally posted by 454newbie View PostComment
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I think I'm missing something here. Both Ampure and the PCR clean seem to do similar things, namely bind fragments larger than a small size cutoff. How do these gel free methods deal with getting rid of large fragments? Do they just rely on having a very tight distribution of fragments to start with? I'd think chimeric molecules would still be an issue even so.
Originally posted by nextgen View PostComment
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Size selection method was published first about adjusting PEG and salt concentration to cause the selective binding of DNA molecules with certain size. The Ampure method used beads to replace centrifugation, which was kind of obvious as Amersham had an earlier patent disclosing using magnetic beads for DNA isolation. In combination with this published PEG method, you can naturally come up with the size selection method with magnetic beads. However, PEG based method is also DNA concentration related as it is essentially a precipitation method. If you have a high concentration of DNA that you don't want, it will carry over to next fraction albeit at reduce concentration. If you have a more selective method, the carryover will be much lower. That is where PCRClean performs better.
Originally posted by greigite View PostComment
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Check this out for automated 454 general library prep:
"A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454"Comment
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