How can I set up auto-analysis for data in GeneMapper with the 3500 Data Collection Software version 3.x?
Beginning with 3500 Data Collection Software version 3, the 3500 Data Collection Software does not support automatic secondary analysis. This is also indicated in the software release notes. To perform secondary data analysis, you will need to manually import the .fsa file into the GeneMapper software. For optimal performance, we recommend that you install the GeneMapper Software on a stand-alone computer that is not part of the 3500 Genetic Analyzer system.
Find additional tips, troubleshooting help, and resources within our Fragment Analysis Software Support Center.
When I started my run on the Applied Biosystems 3500/3500xL Genetic Analyzer, an error occurred: "Unstable Electrophoresis current detected, check for air bubbles" but I don't see any bubbles. What else can cause this?
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. Running Buffer that was:
-On the instrument longer than 2 weeks
-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 the wash the pump chamber and channels wizard using the conditioning pouch and place fresh, non-expired polymer and fresh Anode and Cathode buffer containers. If the problem persists, a service call may be required.
Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.
Do I need to replace the buffer every 14 days if the Applied Biosystems 3500/3500xL Genetic Analyzer is not in use?
If the instrument is not in use, it is not necessary to replace the buffer every 14 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 containers prior to starting a new run.
Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.
Do I need to upgrade or update any secondary analysis software so that it is compatible with 3500/3500xL Data Collection Software v3.1?
If you are upgrading from 3500/3500xL Data Collection Software v1, new Windows 7-compatible secondary analysis software will be required. For all users, if you are going to be using the 36 cm array for sequencing or the 50 cm array with POP-6 polymer and BigDye Terminator v3.1, you will need to apply patches for Sequencing Analysis Software v6, Variant Reporter Software v2 and SeqScape Software v3. You can download the patches from: http://www.thermofisher.com/datacollection3_1.
Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.
Since the 36 cm array is now enabled to do sequencing and fragment analysis, will the 36 cm array be included in the 3500/3500xL system package during purchase?
No, the 36 cm array will not be included in the system package. The standard offering will still be the 50 cm array. If you would like the 36 cm array, it is available for purchase separately.
Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.
