We are currently working through the TruSeq protocol to prep gDNA for hybridization to Nimblegen probes and PE sequencing on a GAIIx... Our problem is that we attempted using Invitrogen's eGels for size selection instead of the recommended gel excision (we have the reagents in-hosue). The bands on the gel were very weak and looked to be out of the size range. I spoke with someone at Illumina about the issue and they claimed to have the same problems when using egels. Has anyone had any success/experience with TruSeq and egels?
Also, we would prefer to use Qiagen cleanup instead of bead cleanup. Has anyone attempted this with TruSeq?
Thanks for any information!
BTS
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