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   & Fragment Analysis
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Located in rooms
B065 and B017




** Below are examples of the most common errors found in Bioanalyzer traces. This guide will help you understand your data better. If you have any questions or concerns about your data, please contact us at panbioanalyzer@stanford.edu.

** For further analysis of your samples, you can use the Agilent 2100 Expert Software to open the raw (.xad) data file.

RNA Assays

** General

DNA Assays

** General
** NGS samples


RNA Assays - (back to top)

Total RNA Integrity –   Spikes – Microparticles and/or air bubbles in the system





Broad Peaks – Sample contaminated with genomic DNA   Missing Peaks – Sample salt concentration is too high





Missing RNA Fragments – Sample salt concentration is too high   Wavy Baseline – contamination with genomic DNA





DNA Assays - (back to top)

** General --

Spikes –mechanical spikes are resulted from microparticles or air bubbles present in the system.  These spikes, in general, do not affect the quality and/or quantity of the sample.   Missing Upper Marker – may be caused by high salt concentration, ethanol contaminants and/or restriction enzymes present in the sample.




Missing Peaks – Sample salt concentration is too high   Baseline Dips – Sample concentration is too high or a contaminant is present




Peak Tailing – Sample concentration is too high






** NGS Samples -- (back to top)

High Molecular Weight DNA Contamination   Split Peaks – sample concentration is too high



Excess Adapter - Inefficient ligation due to too much input DNA or the use of incorrect ligation temperature (ligation is performed at 20-25°C)
  Primer Dimers and PCR Artifacts -



Bead Carried Over –
  Excess primer -




** References and Helpful Links - The summary above is based on the following resources. You can check them out for more details.