Bio-Rad Experion DNA Analysis Kits - Manual (Page 46)

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Error Probable Cause Recommended Action
Peaks are small, broad, or
missing in some samples,
but present in other samples
on the chip Contaminants are present Prepare samples in a different buffer or dilute them in water,
if necessary
Do not use autoclaved water for diluting samples or
ladder. Use only high-quality 0.2 µm-filtered water (such as
Experion DEPC-treated water)
Late migration (peaks
broaden and are delayed
over the course of the run) Turn analysis off (see Section 6.7, Turning Analysis Off, for
more information). Late migration is indicated if there is a
drift in the migration of the lower marker across the chip and
the upper marker migrates later and runs off the top of the
gel view. Refer to the troubleshooting tips that follow
Stop the run, remove the chip, and use a clean pipet tip to
remove or dislodge the bubbles, or remove and replace the
solution in affected wells
When pipetting, insert the tip vertically and to the bottom of
the well. Dispense liquids slowly. Do not expel air at the end
of the pipetting step. Dispense only to the first stop
Air bubbles are interfering with electrical
contact in one or more of the wells
Peaks migrating faster than
usual; electropherogram
appears compressed Electrophoresis station temperature is
inappropriate or fluctuating during the run
(should be 30–35°C); there is no cooling
unit in the electrophoresis station, so if the
temperature changes during the course of a
run, the samples exhibit different separation
characteristics Ensure the temperature of the room is appropriate and
stable, and place the electrophoresis station away from all
heat sources, such as windows or ovens
Sizing is incorrect DNA ladder peaks and upper and lower
markers were improperly assigned by the
software Exclude peaks (follow the instructions in Section 6.3,
Excluding a Peak From Analysis) or manually assign markers
(follow the instructions in Section 6.2, Manually Setting a
Marker), if necessary
Quantitation is incorrect Upper and lower markers were not properly
assigned by the software Check that both markers were properly assigned. Manually
select the marker(s), if necessary (follow the instructions in
Section 6.2, Manually Setting a Marker)
Pipetting and/or dilution errors occurred during
sample preparation or chip loading Ensure calculations and dilutions are correct
Ensure pipets are calibrated, and use pipets that accurately
deliver volumes of ≤10 µl
Do not modify the sample preparation and loading protocols
described in this manual
Ensure that the total DNA concentration of samples is within
the linear dynamic range before proceeding with the sample
preparation instructions described in Section 3.4; if total
DNA concentration is unknown, run a DNA analysis of a
dilution series of the sample
Review the essential practices described in Chapter 2
before initiating another analysis with a new chip
Samples are old or have not been stored
properly, and the DNA degraded Prepare fresh samples and try the analysis again
DNA is <100 bp Small DNA fragments may bind dye differently, depending
on base composition
Ghost peaks or
contaminants appear in
electropherograms Electrodes are contaminated Follow the deep cleaning procedure described in Appendix
B and the software Help section (search term “electrodes”)
Use only 0.2 µm-filtered water (such as Experion DEPC-
treated water) for diluting DNA samples and the DNA ladder;
do not use autoclaved water
Experion Automated Electrophoresis System