scriptseq mrna library prep problem

[dblyons]

I have used the epicentre scriptseq kit to generate barcoded cdna libraries that I will sequence via illumina's hiseq. I am pleased with the fragmentation with this kit-- I performed 18 cycles of amplification and have an obvious product at ~300bp. I used an spri beads (agencourt ampure xp) to clean these up following the PCR, but the bioanalyzer reports that I have two very discrete bands, one peaks at roughly 600bp and the other at the expected 300bp.

I ran the product on a gel to purify the 300bp fragments. I bioanalyzed again and see the same 2 peaks.

Any ideas about what the longer band would be greatly appreciated.

-Dave

[kzueckert]

This observation, concatemers forming from complimentary ends, has also been made with TruSeq libraries:

http://seqanswers.com/forums/showthread.php?t=10883&highlight=truseq

http://seqanswers.com/forums/showthread.php?t=8894

Regards,
-Karin