3130 Genetic Analyzer (factory refurbished) - FAQs

The Water Trap is located above the piston on the pump. There are 2 valves for the trap, one that points out towards you, the other points to the left. To clean the trap:

1) Loosen each of the valves by turning them half a turn counterclockwise.

2) Fill a 5 ml syringe with 4 ml of distilled water.

3) Attach the syringe to the valve extending towards you.

4) Holding a beaker under the valve pointing to the left, push through 3 ml of water. Do not completely empty the syringe to avoid introducing an excessive amount of bubbles into the Water Trap.

5) Tighten the valve pointing to the left and carefully remove the syringe. After removing the syringe, tighten the valve it was attached to. Note: The white end of the valve and grey body should not be separated. If you notice the white piece moving as you try to remove the syringe, re-tighten the syringe and secure the white piece before unscrewing the syringe.


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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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The Polymer Delivery Pump (PDP) and lower block, polymer channels, and tubing can and should be cleaned with all hardware components on the instrument. Run the Water Wash Wizard to clean the pump block, lower block, polymer channels, and polymer tubing. This should be performed monthly or as needed. The Water Trap should be flushed on a weekly basis.

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A few small bubbles are acceptable; however, it is still a good idea to flush the "Water Trap" if there is any doubt. Excessive bubbles will decrease the efficiency of the "Water Trap" from keeping polymer out of the PDP mechanism. The "Water Trap" should be flushed weekly with a good, clean source of distilled/deionized water. Refer to FAQ "Where is the Water Trap and how do I clean it?"

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The "Water Trap" is a circular chamber situated within the Polymer Delivery Pump (PDP) block designed to ensure the PDP integrity/lifetime. This chamber sits on a horizontal axis directly behind the front-facing Luer fitting and encircles the PDP piston. The "Water Trap" acts as a barrier to keep the PDP mechanism (above the trap) isolated from the polymer (below the trap). A small amount of water in the trap dilutes any polymer that moves into the "Water Trap" during normal function of the PDP piston. Proper maintenance, which includes flushing the "Water Trap" with fresh water weekly, ensures that the diluted polymer is removed, along with any bubbles that may have formed. The "Water Trap" holds approximately 325µl of water. Refer to FAQ "How and When to Clean the "Water Trap".

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A spatial calibration is a "map" of where the capillaries are positioned relative to the CCD camera. An accurate spatial is required to ensure accurate data is collected. It is very important to carefully review the results of each spatial calibration to ensure proper mapping/correct identification of each capillary within the spatial run.

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A spectral calibration is an algorithm applied to raw data, which converts it into the component 4 or 5 dye data stored in the sample files. A spectral is created for a specific dye set (combination of dyes), array type (4 or 16 capillaries), and array length (36cm or 50cm). It is used to correct for the natural overlap of the fluorescent dyes.

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We have used Norton AntiVirus software in our testing environment.

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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.

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Yes, Applied Biosystems 3130 Series Systems use the same POP-7 Polymer as Applied Biosystems 3730 series instruments, but is sold in a convenient 7 mL volume bottle which is aligned with expected Applied Biosystems 3130 Series throughput. We do not recommend customers purchase the Applied Biosystems 3730 series sized POP-7 Polymer due to the difference in throughput, limited shelf life and potential problems with pouring.

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All Applied Biosystems 3130 Series documentation, which includes Product Bulletins, Application Notes, Fact Sheets, User Guides, User Bulletins, etc. can be downloaded from our website. For the latest documentation, please go to http://www.thermofisher.com →Technical Resources→Manuals & Protocols.

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DS-02 (Dye Set E5), DS-30 (Dye Set D), DS-31 (Dye Set D), DS-32 (Dye Set F), and DS-33 (Dye Set G5) are all supported on the Applied Biosystems 3130 Series systems. Please refer to the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (http://tools.thermofisher.com/content/sfs/manuals/cms_041468.pdf) for more information.

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The improved basecalling algorithm (the KB Basecaller) is designed to accurately call more bases out of sequencing data, and reduce manual data review time by providing per-base quality value (QV) assignment, which is a measure of basecaller accuracy. The KB Basecaller supports most chemistries and run modules available on the Applied Biosystems 3130 Series Genetic Analyzers running Data Collection v3.0 and v.3.1 Software, and is also integrated in the Applied Biosystems Sequencing Analysis v. 5.X Software and SeqScape v2.X Software. In previous versions of Data Collection Software, resolution performance for all run modules was calibrated with a 98.5% basecalling accuracy (1.5% probability of error) specification using the ABI Basecaller. Utilizing the KB Basecaller v1.2 release for Data Collection v3.0 Software, resolution performance for the all the run modules was calibrated with a quality score cutoff of QV20 (99% basecalling accuracy or a 1% probability of error) using a sliding window of 20 bases from the 3' end. Therefore, while shorter read length specifications are generated with the KB Basecaller, the calibrations are of higher basecalling accuracy. In this release, we are using the same specifications for 98.5% basecalling accuracy, which is on the conservative end, to keep the specifications uniform.

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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.

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The Instrument serial number can be found on the back or bottom side of most instruments. For easier customer access, Thermo Fisher Scientific has produced adhesive holders that can be used to display the serial number and history log on the front or side of your instrument. To obtain a holder, please contact your local service engineer, field application scientist or call technical support.

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It looks like you may have chosen the 6-dye license renewal instead of the BASE license renewal option from the software.

For detailed instructions on renewing the license on the Applied Biosystems 3130 and 3730 Series DNA Analyzers, please refer to the Applied Biosystems 3130 Series Genetic Analyzers and 3730 Series DNA Analyzers: Renewing the Software License (Data Collection Software v.4) Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3730-3130-License-Renewal.pdf). Be sure you are logged onto the computer with Administrator rights before attempting to install the software license file.

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A patch is available here(http://resource.thermofisher.com/pages/WE28396/) to fix this.

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You can purchase a computer for installation of the secondary analysis software packages (e.g., Sequencing Analysis, GeneMapper software) as long as the computer meets the software computer requirements (for processor speed, the minimum speed of the processor should be at least 3 GHz). In these cases, you can install the software yourself.

For the instrument computer, the computer system has a much more stringent requirement and undergoes thorough testing to make sure it can handle the flow of data from the instrument to the computer. The images for the computer system are streamlined to make sure they have the proper drivers for the computer components, and the Operating System is optimized to make sure there is nothing running in the background that might slow the computer down, take up memory, or conflict with our software. Purchasing a computer commercially can introduce too many variables in terms of hardware and software that can negatively affect the data collection process so we cannot support connecting it to the instrument.

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Installation of the Data Collection Software for the Applied Biosystems 3130/3130xl Genetic Analyzer is a complex process that requires a Field Service Engineer to install the software properly.

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It is possible that the instrument and computer had a communication issue, disassociating the data from the plate record, resulting in no history and no data files. If this happens, shut down the instrument and the computer, wait 2 minutes and restart the system following the instructions in the Applied Biosystems 3130/3130xl Genetic Analyzers: Starting Up the Instrument Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Start%20Up%20Procedures.pdf) or the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4)(https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).

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When placing the array on the instrument, the last step in the process is to loosen the array knob and the instrument forces any air bubbles around the array tip through the threading and the middle of the array knob. Some polymer gets pushed through as well and when it dries up, it appears as a white, flaky residue. Use a damp, lint-free cloth to remove it. If more residue appears after the cleanup, it is possible that the array knob is not tightened enough or the array ferrule may require replacement.

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If the array is stuck in the pump, even after loosening the knob, squirt around the edge of the array head with distilled water and try to remove it again. If the array will not move, a service call may be required. Do not use excessive force or tools to try and remove it.

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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.

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It is not unusual to see a large bubble at the tip of the piston while performing the water wash wizard on the system. When the polymer is put back on to the system, the difference in viscosity is usually enough to dislodge the bubble and push it out. In extreme cases, it may be necessary to repeat the wash and go back and forth between the water and polymer to force it out.

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If the system has not been started in the last week, completely shut off the instrument and the computer, wait for 2 minutes and restart it as directed in the Applied Biosystems 3130/3130xl Genetic Analyzers: Starting Up the Instrument Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Start%20Up%20Procedures.pdf) or the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4) (https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).

If the computer itself seems to be running slowly after restarting, you may need to defragment the hard drives. For the Applied Biosystems 3130/3130xl Genetic Analyzer, only defragment the C and E drives. Do not defragment the D and F drives - the Oracle database is installed on these drives, and defragmenting the Oracle drive may cause functionality issues with your Data Collection and GeneMapper software.

If the system has been restarted and the computer slowdown is limited to the instrument Data Collection Software, it is possible that the database/data store is getting full. For the Applied Biosystems 3130/3130xl Genetic Analyzer, after the Data Collection Software has launched, select “Database Manager” on the left side. If there are more than 300 runs or the database is greater than 10% full, you will need to click the Cleanup button to remove all Processed plates in order to increase the speed of the system. Should the database remain this way or continue to get filled, it will eventually hit a point where it will lock up and a service call will need to be opened for re-imaging and re-installation.

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-Completely shut down the instrument and computer. Wait 2 minutes and restart the computer, log in, then turn on the instrument and wait for the green light.
-Right click on “Computer” and select “Manage”. Expand “Services and Applications” and click on “Services”
-Scroll down to “Oracle” in the list on the right. Any Oracle service that has a startup type of “Automatic” should have a Status of “Started”. If not, select the service and click Start. After the services have started, wait 2 minutes and then try to launch the Data Collection Software.

If the services do not start or if the issues are not resolved, please contact Technical Support at techsupport@thermofisher.com for further assistance. This symptom may require a service call.

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The location of the files is determined by the Results Group. Double check the Location tab in the Results Group selected for the run to make sure it has not been changed and the files saved to a different location.

On the Applied Biosystems 3130/3130xl Genetic Analyzer, you can click on Run History in the Data Collection Software, select your plate and go to the Re-extraction heading under Run History to try and recover the data files.

Some other causes of missing data include:

- If the system is networked and something interrupts the network connection then it might interrupt the connection between the instrument and the computer. Depending on when it occurred, you might be able to recover it on Re-extraction. If you are saving the samples to a network drive and the location is unavailable, the data may still be in the Oracle Database on the Applied Biosystems 3130/3130xl Genetic Analyzer and can be re-extracted.
- The Event Log might show that the run aborted due to the user aborting it, so the run will appear to have completed or stopped with no errors and no data. A possible cause is septa that is old/re-used. Septa can become sticky and gummy over time and eventually start sticking to the array. In the best case scenario, the array will lift the plate off of the autosampler just enough to break the connection with the plate sensor and abort the run. Worst case scenario is that the plate remains on array as the autosampler starts to move, bending the electrodes and breaking the array. We officially recommend that the plate septa be used one time only. Re-use of septa can result in contamination and sample degradation. However, we are aware that some of our customers will rinse the septa with water and re-use them. If choosing to re-use septa, do not use bleach, detergents, or solvents to clean the septa, it will cause them to dry out faster and risks contaminating the system.

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“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.

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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.

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A perpetually blinking amber light usually indicates that there is a door open on the instrument or a bad door sensor. Open the main door, the oven door, and the detector cell door (small black door with the laser warning on it) and close them again. After the autosampler stops moving, the light should change to green. If the amber light does not go to green, it is possible that a door sensor is not working properly and a service call may be required.

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The amber light starts to blink once the instrument has logged onto the computer using the User account (e.g., 3130User). Anything that prevents it from connecting will cause the amber light to remain solid. Some of the more frequent reasons for this happening include:

-User password has expired or changed
-Firewall is on
-Cable is plugged into the wrong port
-The wrong network card was configured to connect to the local network
-Bad network card


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A blinking red light on the instrument may indicate that a hardware component has failed or a possible communication disruption has occurred between the instrument and computer. Completely shut down the instrument, wait for 2 minutes, and then start up in the order documented in the Applied Biosystems 3130/3130xl Genetic Analyzers: Starting Up the Instrument Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Start%20Up%20Procedures.pdf) or the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4)(https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).
If the instrument goes from a flashing amber light to red light, one or more of the hardware components has failed the hardware diagnostic, and a service call should be opened up.

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The initial software registration is performed with your Field Service Engineer during the instrument installation. Once the initial registration is done, you will need to renew the license annually. There is no cost associated with renewal, just a computer with internet access and email access.

For detailed instructions on renewing the license on the Applied Biosystems 3130/3130xl Genetic Analyzer, please refer to the Applied Biosystems 3130 Series Genetic Analyzers and 3730 Series DNA Analyzers: Renewing the Software License (Data Collection Software v.4) Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3730-3130-License-Renewal.pdf).

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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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If you map the network drive so it shows up under Computer as a drive letter, then this feature can be configured from the Instrument Data Collection Software through the Results Group by going to the Destination tab, clicking “custom” and then browsing to the location on the network.

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The instrument computer can be connected to your local network via the second NIC card by your local IT group. We don't offer Technical Support to assist with networking issues, and our warranty and service contract terms exclude coverage for instrument system problems that are caused by the network connection (i.e., computer virus, hacking, updates, or patches that alter the compute environment). However, our field service team will respond during the warranty period and while the instrument is covered by an AB Assurance service contract to isolate the cause of any problem either with instrument hardware, software, chemistry, or that arises from an external environmental source including the connection to a customer-owned internal network. Beyond that we can escalate issues to a product technical team who can review instrument logs and advise on the nature of the problem in an effort to help customers find and correct the source of the problem. For tips on connecting your computer to the local network, please see the Instrumentation Networking Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/Instrumentation-Networking.pdf).

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All of our systems have been tested with Norton Anti-Virus Software.

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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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If the instrument is not in use, it is not necessary to replace the buffer every 2 - 3 days. However, the buffer level needs to remain at the fill line to prevent the capillary or array from drying out. Top off the buffer volume with water if necessary. Replace the anode and cathode buffer with freshly made 1X Running Buffer prior to starting a new run.

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Maintenance tasks on the Applied Biosystems 3130 Series Genetic Analyzer are broken down into daily, weekly, monthly, and as-needed tasks. For detailed information on the maintenance steps and when to perform them, please refer to the Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance Checklist(https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Maintenance%20Checklist.pdf) or the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4)(https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).

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The Data Collection and secondary analysis software requires certain permissions in order to function (Read, Write, Delete). To avoid issues with restrictions placed on user accounts, it is recommended that you log in either as Administrator or INSTR-ADMIN.

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There is no harm in restarting the system daily, but it should not be necessary unless there is an occasional loss in communication between the instrument and computer or the system is running significantly slower than normal. If the problems in run speed or communication loss are persistent, then it may be indicative of a larger problem. Technical Support should be contacted for further assistance at techsupport@thermofisher.com.

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We recommend that you restart the system once a week. The system may require a restart more frequently if you experience issues related to a communication interruption between the instrument and computer. Some systematic issues include:
-The software freezing or becoming unresponsive
-The run timer not counting down or flashing back and forth between two different times
-No data present at the end of the run

In the event of a communication issue between the instrument and computer, close the Data Collection Software (perform a forced shutdown of the application through the Task Manager if Data Collection is unresponsive), completely power down the instrument and turn off the computer. To properly clear the memory, power down the system for at least 2 minutes prior to a restart.

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After performing the short-term or long-term shutdown wizards:

1. Click “Stop All” in the Service Console and wait until all 4 services turn green. Close the program.
2. Go to the Start menu and select Shut Down. On Windows 7, click the Windows icon in the lower left corner of the screen. Click the arrow next to “Sleep” and select “Shut Down”.
3. Click the power button on the instrument.

Step-by-step instructions for the shutdown procedures can be found in the Applied Biosystems 3130/3130xl Genetic Analyzers: Shutting Down the Instrument Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Shut%20Down%20Procedures.pdf) and the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4)(https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).

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For the Applied Biosystems 3130/3130xl Genetic Analyzer, if the instrument will be idle for less than a week, perform the short-term shutdown of the system. If it will be idle for longer than a week, follow the instructions in the user guide for a long-term shutdown using the Instrument Shutdown Wizard.

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The Applied Biosystems 3130/3130xl Genetic Analyzer system includes both the instrument and the computer - you cannot start or restart one without starting the other. Improper boot sequence can lead to communication issues, aborted runs, and possible loss of data. The proper boot sequence is:

1. Turn on the computer and log in as the local administrator.
2. Turn on the power button on the instrument and wait for the green light.
3. Launch the Data Collection Software and wait until all 4 services turn green.

Step-by-step instructions for the start-up procedures can be found in the Applied Biosystems 3130/3130xl Genetic Analyzers: Starting Up the Instrument Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3130%20Start%20Up%20Procedures.pdf) and the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4)(https://tools.thermofisher.com/content/sfs/manuals/4477796.PDF).

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