Ladder-like Bioanalyzer trace on TruSeq RNA libraries

[egunth]

Hi all, I just completed the Illumina TruSeq RNA v2 protocol and my end product gave a bioanalyzer trace that looks like there's some sort of DNA ladder contamination in the preps. The issue is, no ladder of any sort was used in this protocol so I'm not sure exactly where something like that would come from. Has anyone seen a BA trace like this after a TruSeq prep? I started with 1 ug of whole RNA for each sample and did subsequent purifications with Ampure XP beads, not gel extraction. Any insight would be greatly appreciated.

Thanks

[Jon_Keats]

Sure you don't only have the inline spike-in controls. What did the template RNA look like?

[egunth]

I did use the in-line controls, is that what they look like on a bioanalyzer? The RNA looked very nice. We opted to forgo an RNA bioanlyzer trace but all samples looked clean on denaturing gel, nanodrop trace, and were confirmed by RT-PCR.