When I started my run on the Applied Biosystems™ 3730/3730xl DNA Analyzer, an error occurred: “Leak detected” but I don't see any leaks. What else might cause this?

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Answer

“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.

Answer Id: E12746

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After my run finished on the Applied Biosystems™ 3730/3730xl DNA Analyzer, I don't see any data files. Where is my data?

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Answer

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™ 3730/3730xl DNA 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.
-If the septa is old/re-used. We officially recommend that the plate septa be used one time only. However, we are aware that some of our customers will rinse the septa with water and re-use them. In those instances, the 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. 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. Worst case scenario is that the plate remains on array as the autosampler starts to move, bending the electrodes and breaking the array. Replace the plate septa regularly (each run is recommended, but after no more than 4-5 rinses; no not use bleach, detergents, or solvents to clean the septa, it will cause them to dry out faster and risks contaminating the system).

Answer Id: E12747

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How often should I restart my Applied Biosystems™ 3130/3130xl Genetic Analyzer?

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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.

Answer Id: E12691

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The amber light on my Applied Biosystems™3500/3500xL Genetic Analyzer continues to blink and won't proceed to green like it normally does. What's wrong?

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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 light does not go to green, it is possible that a door sensor is not working properly and a service call may be required.

Answer Id: E12777

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For my Applied Biosystems™ 3730/3730xl DNA Analyzer, the data service will not go to green. What should I do?

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1.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.
2. Right click on “Computer” and select “Manage”. Expand “Services and Applications” and click on “Services”
3. 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 this does not resolve the issue, please contact Technical Support at techsupport@thermofisher.com for further assistance. This symptom may require a service call.

Answer Id: E12748

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Can I restart my Applied Biosystems™ 3130/3130xl Genetic Analyzer daily?

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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.

Answer Id: E12692

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With my Applied Biosystems™ 3130/3130xl Genetic Analyzer, I seem to be getting bubbles from the polymer bottle but the polymer level is normal. What is causing it?

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Answer

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.

Answer Id: E12716

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The Integration Service won't start on my Applied Biosystems™3500/3500xL Genetic Analyzer. Why?

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Answer

The reasons for this will vary depending on what version of Applied Biosystems™3500 Data Collection Software you are using:

For the Applied Biosystems™3500 Data Collection Software v.1.0, v. 1.1 and v.2.0, the TxnPassStore.dat file may have become corrupted. To fix:

-Right click on the Integration Service icon in the lower right corner of the screen and select “Exit”. -Go to D:/Applied Biosystems/3500/webMethods/IntegrationServer/config -Right click on the TxnPassStore.dat file and select “Restore Previous Version” -Select the most recent version from before the problem started and click “Restore”. -When the roll back is complete, click OK and restart the computer and the instrument in the order in the User Guide or Technical Note on Starting up the system.

For the Applied Biosystems™3500 Data Collection Software v.3.0, v. 3.1, the Integration Service no longer relies on web Methods in these versions of Data Collection. Most cases of the -Integration Service not launching has been tied to changing the computer name after the software was installed or upgraded. Changing the computer name back to its old name will resolve the problem.

Answer Id: E12778

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It is taking a longer time to start the Applied Biosystems™ 3730/3730xl DNA Analyzer Data Collection Software, what should I do?

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Answer

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 in the order in the Applied Biosystems™ 3730/3730xl DNA Analyzers: Starting Up the Instrument Technical Note or the Applied Biosystems™ 3730/3730xl DNA Analyzer Getting Started Guide.

If the computer itself seems to be running slowly after restarting, you may need to defragment the hard drives. For the Applied Biosystems™ 3730/3730xl DNA 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's possible that the database/data store is getting full. For the Applied Biosystems™ 3730/3730xl DNA 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.

Answer Id: E12749

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How do I shut off my Applied Biosystems™ 3730/3730xl DNA Analyzer?

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Answer

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™ 3730/3730xl DNA Analyzers: Shutting Down the Instrument Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3730-Shut-Down-Procedures.pdf) and the Applied Biosystems™ 3730/3730xl DNA Analyzer Maintenance and Troubleshooting Guide (http://tools.thermofisher.com/content/sfs/manuals/3730SR_3730XLR_4359473_Maint_TroubShoot_UG.pdf).

Answer Id: E12725

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How long can I keep the buffer on the Applied Biosystems™3500/3500xL Genetic Analyzer?

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Answer

For the Applied Biosystems™3500 Series Genetic Analyzer, the buffer will keep for 14 days if room temperature is <25 degrees C and for 7 days if >25 degrees C.

Answer Id: E12766

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Which login should I use for the Applied Biosystems™ 3130/3130xl Genetic Analyzer computer?

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Answer

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.

Answer Id: E12693

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Can I purchase a computer from you or someone else and install the Applied Biosystems™3500/3500xL Genetic Analyzer software myself?

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Answer

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 compute requirements (for processor speed, the minimum speed of the processor should be at least 3 GHz) and 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.

Answer Id: E12787

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Can I use Applied Biosystems™ 3730 DNA Analyzer 10X Running Buffer on the Applied Biosystems™ 3130/3130xl Genetic Analyzer?

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Answer

We do not recommend mixing and matching the various instrument reagents as each is manufactured using different processes, tested as an entire system, and warrantied to perform to a minimum specification. Substituting reagents can compromise the integrity of the system and cannot be supported by our service or support specialists. In addition, the 10X Running Buffer expires 1 year after date of receipt and once diluted to 1X, it will last 30 days at 2 - 8 degrees C or 7 days at ambient temperature. This could potentially result in having to dispose of a large volume of 10X Running Buffer due to expiration if you are using it on a lower-throughput system.

Answer Id: E12701

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What is a spectral calibration?

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Answer

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.

Answer Id: E2530

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