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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 and the Applied Biosystems™ 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4).

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.

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 and the Applied Biosystems™ 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4).

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. 

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

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.

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 or the Applied Biosystems™ 3130/3130xl Genetic Analyzers Getting Started Guide (Data Collection Software v.4).

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

For the Applied Biosystems™ 3130/3130xl Genetic Analyzer, the buffer can keep for 48 hours.

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.

Putting the polymer back at 2–8°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.

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.

The arrays are warrantied for a certain number of runs or one year from date of receipt, whichever comes first. If you notice that you are starting to get reduced data quality (e.g., shorter reads, trailing peaks in all 4 colors) even with the Sequencing Standard, these may be signs that the array requires changing. 

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°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. 

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. 

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. 

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

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 Software Licensing Technical Note.