Size Select Protocol without using Gel

[zeineen]

Hi,
Is there any method out for a large quantity of DNA size selection,
something like with 96-well plate. The traditional way is to excise
agaroase gel and do DNA purification, but it's too labor-intensive for
hundreds of samples.
Do any have protocol which follows Ampure beads for Size selection for
high throughoutput samples.
It would be great if someone can help me out.

[TUCF JSS]

There has been reported lot-to-lot variations in AMPureXP bead's size selection. Therefore for each new lot you get you should perform a titration experiment on a 50-100 bp ladder at a fixed volume. Vary only the amount of AMPureXP beads you put in each (in increments of 0.1 or so), and run a gel or Bioanalysis to see the ideal concentrations for size exclusion of particular fragments.

For a protocol which has been worked out for high throughput sequencing you can simply view the Illumina protocol for their DNA Library prep kit (TruSeq).

http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

Good luck!