Observation
Possible cause
Recommended action
Poor resolution in some
capillaries
Poor-quality samples were
used.
See “Sample preparation guidelines“ on
page 37.
Use a control sample to determine if the poor
resolution is due to the samples are another
factor.
A capillary was damaged or is
blocked.
Try to clear the capillary, then replace the
cartridge if the poor resolution is due to the
cartridge and not the sample.
1. Touch Settings
4
Cartridge
4
Cartridge
maintenance
4
Fill array.
2. Touch when the function ends.
3. Run a control sample.
Poor resolution in all the
capillaries
The cartridge has been used for
more than the stated number of
injections, is past the labeled
expiration date, or has
degraded polymer from
incorrect storage.
Replace the cartridge.
The Hi
‑
Di
™
Formamide that was
used to prepare the samples
was degraded.
Prepare the samples with fresh Hi
‑
Di
™
Formamide and repeat the reaction.
See:
• “Sample preparation guidelines“ on
•
DNA Fragment Analysis by Capillary
Electrophoresis User Guide
(Pub. No. 4474504)
There was too much sample
injected.
Dilute the sample and re-inject it.
Spikes are present in raw
and/or analyzed fluorescence
data
Trace impurities passed the
detector.
For fragment analysis, increasing the
Minimum peak half width setting in the
analysis settings (under Common settings) can
reduce the identification of spikes as peaks.
Note:
Secondary sequencing and fragment
analysis software can recognize and ignore
spikes.
Repeat the injection if necessary.
There is noise in the baseline
Fluorescent contamination has
built up in the CBC.
Replace the CBC. Use a new reservoir septum
when assembling the new CBC.
Sample carryover from a
previous injection
Sample carryover on the
SeqStudio
™
Genetic Analyzer
can occur in trace amounts
when previous injections are
off-scale. Very strong peaks, for
example, primer peaks in a
fragment analysis sample, are
typically visible in subsequent
injections.
Replace the reservoir septum on the CBC
before the next injection to minimize the
carryover effect.
Appendix A
Troubleshooting
Sample and data troubleshooting
A
SeqStudio
™
Genetic Analyzer Instrument and Software User Guide
177
