Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer User Manual page 177

Observation
Poor resolution in some
capillaries
Poor resolution in all the
capillaries
Spikes are present in raw
and/or analyzed fluorescence
data
There is noise in the baseline
Sample carryover from a
previous injection
SeqStudio Genetic Analyzer Instrument and Software User Guide
™
Possible cause
Poor-quality samples were
used.
A capillary was damaged or is
blocked.
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.
The Hi‑Di Formamide that was
™
used to prepare the samples
was degraded.
There was too much sample
injected.
Trace impurities passed the
detector.
Fluorescent contamination has
built up in the CBC.
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.
Appendix A Troubleshooting
Sample and data troubleshooting
Recommended action
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.
Try to clear the capillary, then replace the
cartridge if the poor resolution is due to the
cartridge and not the sample.
1. Touch Settings4Cartridge4Cartridge
maintenance4Fill array.
2. Touch when the function ends.
3. Run a control sample.
Replace the cartridge.
Prepare the samples with fresh Hi‑Di
Formamide and repeat the reaction.
See:
• "Sample preparation guidelines" on
page 37
• DNA Fragment Analysis by Capillary
Electrophoresis User Guide
(Pub. No. 4474504)
Dilute the sample and re-inject it.
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.
Replace the CBC. Use a new reservoir septum
when assembling the new CBC.
Replace the reservoir septum on the CBC
before the next injection to minimize the
carryover effect.
A
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