Automated size fractionation of samples or libraries

[james hadfield]

Has anyone tried any of the automated size fractionation systems that are out there? They look like they could simplify and standardise a process that users spend a lot of time and effort on and as the number of libraies goes up gels are certainly not flavour of the month.
We have thought about bead based cleanup and size selection but the range is quite broad which does not fit all applications as well (miRNA, Structural Variation).

Pippin Prep: Sage Science

• 4 samples on a ‘chip’
• 60-90 minute run time
• 40ul loading volume and up to 20ug of material,
• not sure on how tightly you can specify the size to collect.
• ‘Bioanalyser’-esque electropherogram

Lab ChIPXT: Caliper Life Science

• 4 samples on a ‘chip’
• 30 minute run time
• Not sure on loading volumes
• No post-purification needed
• Specify size with +/-10% e.g. 298 +/-12bp
• ‘Bioanalyser’-esque electropherogram

[sophie mcquade]

I have a demo unit in my lab right now and I don't want to send it back. You can set it to capture a target size. If you select 300 bp as your target you get 276-324 bp, 8% on either side of your target. Or you can set it to capture an 80 bp range. You are limited by the 40 ul size of the elution chamber. You can also set it on manual mode and stop it anytime, collect the 40 ul from the chamber, start it up again and collect another 40 ul if you want to collect more than an 80 bp size range. Using the 300 bp target I got 40 ul at about 15 ng/ul. This was more than enough to PCR for a sequence capture by array hybridization for next gen seqeuncing. I will send you an image of my gel after the collection and PCR.