POP-6 Polymer for Applied Biosystems Genetic Analyzers, 7000 μL, 960 samples - FAQs

When contacting Genetic Analysis Support (FAS, FSE, Technical Support), we can address your inquiry most efficiently if you have the following information:

- Instrument Model and Serial Number
- Version of the software you are using
- Application and/or Kit Information
- Kit Lot Number
- Number of runs on the Capillary or Array
- Polymer Type and Lot Number
- Buffer Lot Number
- Hi-Di Formamide Lot Number or Loading Solution Information
- Sample data that can be sent to the Support Person

Please also provide details on:
- Reaction set up (i.e. how much DNA was used, Primer, etc.)
- How the reactions were cleaned up (Alcohol precipitation, columns, etc)
- What template DNA was used (i.e. Plasmid, PCR product)
- How was the Template DNA prepared?

All of this information will help the Support representative quickly and accurately assess the problem and provide you with recommendations for resolution.


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POP-7 polymer can maintain its performance for seven days on the Applied Biosystems 3730 Series DNA Analyzer at standard lab conditions. After seven days, perform all required maintenance (including the Water Wash Wizard) and replace with fresh polymer. Do not "top off" the polymer bottle (add fresh polymer to old polymer), which can adversely affect data quality and consumable lifespan.

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Applied Biosystems supports the use of POP-7 polymer on the Applied Biosystems 3730 Series DNA Analyzer. If the instrument is running Applied Biosystems 3730 Data Collection Software v.3.1 or later, then you can also use POP-6 polymer. We do not recommend mixing and matching of various instrument polymers as each is manufactured in different processes, tested as an entire system, and guaranteed to perform to a minimum specification. Substitution of reagents may compromise the integrity of the system and cannot be supported by AB service or applications support specialists. Using unsupported polymers may adversely affect data quality, consumable lifespan, and may void existing warranties.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

On the 36 cm array:

- The UltraSeq36_POP7 run module has a run time of 35 minutes and an average read of 500 bases with a QV >20.

- The RapidSeq 36_POP7 run module has a run time of 60 minutes and an average read length of 600 bases with a QV >20.

- The UltraSeq36_POP4 run module has a run time of 40 minutes and an average read length of 400 bases with a QV >20.

- The RapidSeq36_POP6 run module has a run time of 60 minutes and an average read length of 500 bases with a QV >20.

On the 50 cm array:

- The FastSeq50 _POP7 run module has a run time of 60 minutes and an average read length of 700 bases with a QV >20.

- The StdSeq50 _POP7 run module has a run time of 120 minutes and an average read length of 850 bases with a QV >20.

- The StdSeq50 _POP4 run module has a run time of 100 minutes and an average read length of 600 bases with a QV >20.

- The StdSeq50 _POP6 run module has a run time of 150 minutes and an average read length of 600 bases with a QV >20.

On the 80 cm array:

- The LongSeq80 _POP7 run module has a run time of 170 minutes and an average read length of 950 bases with a QV >20.

- The LongSeq80 _POP4 run module has a run time of 210 minutes and an average read length of 700 bases with a QV >20.



Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

The detection cell heater automatically turns ON at 50°C for all POP-7 default and user created run modules. It is automatically OFF for all POP-4 and POP-6 default and user created run modules. These settings cannot be altered. The mobility files of the various Applied Biosystems analysis applications have been optimized, among other things, based on polymer type and temperature conditions.

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Dedicated capillary arrays for each polymer are not necessary. But if you need to switch polymer types, for example from POP-6 polymer to POP-7 polymer, you would need to use the Change Polymer Type Wizard to ensure good data quality after switching polymer types. A different spectral calibration for each dye set is required for each polymer type.

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We advise that you inspect the polymer bottle for remaining volume before starting a series of runs. We recommend leaving at least 0.5 mL in the bottle before using the Replenish Polymer Wizard to replace the polymer bottle with fresh polymer of the same type and to prevent excessive bubbles going into the pump chamber. If air bubbles are created in the current path, as would occur when polymer is depleted, the system will detect this anomaly before the run begins and an "unstable current, bubble detected" error will be generated and the run stops.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

Yes. POP-7 Polymer is enabled for both Sequencing and Fragment Analysis on the 36 cm and the 50 cm capillary arrays. Using POP-7 Polymer allows longer reads and/or faster runs (in conjunction with the detection cell heater) potentially giving more samples per day compared to using POP-4 polymer and POP-6 polymer.

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The Applied Biosystems 3130 Series uses polymer a little differently than the 3100 series due to a new polymer delivery system. Capillary fill volumes require roughly the same amount of polymer but set up is much different. Applied Biosystems has eliminated the use of manual polymer syringes and replaced them with the new automated polymer delivery system and easy to use set up wizards. Variables such as instrument utilization and instrument set up and maintenance can affect polymer usage. As a result some customers may use slightly less polymer and some customers may use slightly more polymer than on their prior 3100 series system.

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We recommend that the Applied Biosystems 3130 Series polymers be changed on the instrument after one week.

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The POP-4 polymer and POP-6 polymer run modules that were available in the 3100 Series Systems are also available in the 3130 Series Systems. Sequencing Analysis Software and the KB Basecaller also includes Applied Biosystems 3130 series optimized basecaller and mobility files for all polymers. There is also an automated wizard in the Applied Biosystems 3130 series Data Collection Software v3.0 and v.3.1 that allows the user to change between different polymer types. Since the bottles for the 3130 POP-4 polymer, POP-6 polymer, and POP-7 polymer attach directly to the instrument, the 3100 Series POP-4 polymer and POP-6 polymer cannot be used on the Applied Biosystems 3130 Series systems and vice versa.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

The POP-7 Polymer, along with enabling of the detection cell heater, allows faster turn around times, better peak resolution, longer read lengths, and along with KB Basecaller gives higher quality score reads. The POP-7 Polymer also enables using a single polymer for the 36 and 50 cm array lengths for fragment analysis and sequencing applications.

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It is possible that the polymer tube fitting may not be screwed into the pump properly, allowing air to get pulled in as the piston retracts. It is also possible that some debris may be stuck in the check valve, locking it in the open position. It may be necessary to detach and carefully attach the polymer tube again and then perform a water wash wizard to remove the bubbles and clear any debris from the check valve.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

“Leak detected” error messages can also occur when the piston on the pump moves further than expected during the movement of the pump. The usual cause for this is a leak on the system, usually due to either an improperly tightened or improperly threaded fitting or a broken capillary. However, if this is not observed, some of the other reasons are:

1. Valve stuck in open position
2. Large air bubble under the piston
3. Polymer:
- Wrong polymer type (e.g., instrument thinks it has POP-7 on it but it really has POP-4)
- Old/degraded polymer
4. Improper/no maintenance on the system

Inspect the system for leaks. If you do not see any leaks on the system, perform a water wash using the water wash wizard and place fresh, non-expired polymer and freshly made 1X Running Buffer on the system. If the problem persists, a service call may be required.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

Some of the other causes of an Unstable Electrophoresis current detected error message are:

1. Leak on the system
2. Polymer that:
-Has expired
-Has been left on the instrument for more than the recommended time
-Is a mixture of expired polymer and non-expired polymer
3. Using Running Buffer that was:
- Diluted to 1X incorrectly
- Swapped with the water position on the Autosampler deck
- On the instrument longer than 48 hours
- Not filled to the fill line or evaporated below the fill line
4. An arcing event that was not cleaned afterwards using the water wash wizard
5. Not performing regular maintenance on the instrument
6. Hardware issues

Inspect the system for leaks. If you do not see any leaks on the system, perform a water wash using the water wash wizard and place fresh, non-expired polymer and freshly made 1X Running Buffer on the system. If the problem persists, a service call may be required.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

If we do not specify the expiry date or number of uses, the warranty will last for 12 months from the date of shipment.

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Thermo Fisher Scientific can only provide warranty on performance on non-expired reagents. Using reagents past their expiration date is a risk and may compromise your data integrity.

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Putting the polymer back at 2 - 8 degrees C may extend the life of the polymer, however, we do not have any data indicating how long it might extend it. Removing the polymer and putting it back on the system can also result in a trade-off in usage. When placing it back on the system, you will need to degas the polymer for 30 - 60 mins, refill the pump/block, array, and remove bubbles, which will cause you to use more polymer for maintenance than you would for running samples and may decrease the number of runs you can get out of a single polymer bottle/pouch.

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For the Applied Biosystems 3130/3130xl Genetic Analyzer, the polymer can remain on the instrument for a week.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.