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Old 03-08-2012, 04:21 AM   #2
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
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My first guess would be that they are the TruSeq Control fragments. These are an optional component of both RNA and DNA prep kits. They have a variety of sizes and sequences. The HiSeq Control Software (HCS)/Real Time Analysis (RTA) software recognizes their sequence and their relative proportions are plotted in a pane of the Sequence Analysis Viewer (SAV).

I don't use them, so I can't tell you for sure. Under normal circumstances I think they are likely at too low of a concentration to be detectable amongst the background of your sample. But in cases where scant sample is present, they might become alarmingly visible. Could be my imagination, but I think I can see faint peaks of similar sizes in lane 5, for example.

The BioAnalyzer individually scales each lane by default. If you are viewing your data via the Agilient 2100 Expert Software you can turn this behavior off by clicking on the "Gel" tab and the sub-category "Scaling Mode" to choose "Global Scale". I am guessing that if you do this, then the peaks you see clearly in lane 6 will fade into the background. Which indicates the issue is that there is no (or almost no) sample there.

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