Size-selection of TruSeq DNA library

[ageneheo]

I'd like to know how efficiently to do the size-selection of library ligated with TruSeq adapter from the Gel-method.

TruSeq adapter has very long non-hybridized Y-shape form (about 50 nt X 2 = 100 nt at both ends).

Have you had any different results regarding the size of library between size-selection after ligation with adapter and final PCR amplification?

[kwaraska]

yes we did

When we ran them on an e-gel size selection system, they ran incorrectly.

We went to a pippin prep to ensure correct sizing. We now use a robot which does it on beads but they will not give us the concentrations they use to do it, but I'm sure there are publications that give double-sided SPRI size selection.

[Élodie]

I use E-gel SizeSelect 2% from Invitrogen and 50bp DNA ladder. The 350 bp band is brighter than other bands. My samples run correctly and I can easily collect the 300-400bp band.