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Analysis of PowerPlex® Systems using the Applied Biosystems 3500 and 3500xL Genetic...

Analysis of PowerPlex® Systems using the Applied Biosystems 3500 and 3500xL Genetic Analyzers

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Dawn Rabbach

Promega Corporation

Publication Date: 2011

Which dye set do I use with the PowerPlex® Systems? Do I need to switch the F or G5 spectral calibration when switching between Promega and Applied Biosystems products?

One new dye set must be created for the 4-dye PowerPlex® Systems, and one new dye set must be created for the 5-dye PowerPlex® Systems. It is unnecessary to switch spectral calibrations between Promega and Applied Biosystems products because selection of the correct spectral is part of the Instrument Protocol. Creating a new dye set is very simple with the 3500 series data collection software.

  1. To create a new dye set, navigate to the Library, highlight “Dye Sets” and select “Create”.
  2. The Create New Dye Set tab will appear (Figure 1). Name the Dye Set, select “Matrix Standard” for the Chemistry and select “G5 Template” for the Dye Set Template. Select “Save”.
    The Create New Dye Set window.Figure 1. The Create New Dye Set window.

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  3. To perform the spectral calibration with Promega 5-dye chemistries, go to the Maintenance tab, select “Spectral”, and under the Calibration Run tab, choose the appropriate fields: Choose “Matrix Standard” from the Chemistry Standard pull-down menu and the new Promega 5-dye set created in Step 2 (i.e., Promega G5) from the Dye Set pull-down menu (Figure 2).
    The Calibration Run window.Figure 2. The Calibration Run window.

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  4. Select “Start Run”.

Can I use the PowerPlex® Matrix Standards, 3100/3130, for spectral calibration on the Applied Biosystems 3500 Genetic Analyzer?

Yes. For detailed instructions, see the PowerPlex® 5-Dye Matrix Standards, 3100/3130, Technical Bulletin #TBD024.

Do I have to run a new spectral calibration every time an array is changed?

Yes. The old spectral will not be available once the new array is installed on the instrument.

Do I use the same ratio of Internal Lane Standard (ILS) 600 or CC5 ILS 500 to formamide when setting up the formamide plate for the Applied Biosystems 3500 and 3130 Genetic Analyzers?

Yes. We recommend the same ratio for these instruments, but as always, laboratories should perform internal validation to determine the optimal ratio for individual instruments.

Will I have to change the peak window size in the Peak Detector tab of the Analysis Method for GeneMapper® ID-X analysis with the PowerPlex® ESX or ESI Systems run on the Applied Biosystems 3500 Genetic Analyzer?

For the PowerPlex® ESI 16 and 17 Systems, we recommend a peak window of 11 instead of 15. For the PowerPlex® ESX 16 and 17 Systems, the peak window can be kept at the default value of 15.

How to Cite This Article

Rabbach, D. Analysis of PowerPlex® Systems using the Applied Biosystems 3500 and 3500xL Genetic Analyzers. [Internet] 2011. [cited: year, month, date]. Available from: http://at.promega.com/resources/profiles-in-dna/2011/analysis-of-powerplex-systems-using-the-applied-biosystems-3500-and-3500xl-genetic-analyzers/

Rabbach, D. Analysis of PowerPlex® Systems using the Applied Biosystems 3500 and 3500xL Genetic Analyzers. Promega Corporation Web site. http://at.promega.com/resources/profiles-in-dna/2011/analysis-of-powerplex-systems-using-the-applied-biosystems-3500-and-3500xl-genetic-analyzers/ Updated 2011. Accessed Month Day, Year.

Contribution of an article to Profiles in DNA does not constitute an endorsement of Promega products.

PowerPlex is a registered trademark of Promega Corporation.

Products may be covered by pending or issued patents or may have certain limitations. More information.

All prices and specifications are subject to change without prior notice.

Product claims are subject to change. Please contact Promega Technical Services or access the Promega online catalog for the most up-to-date information on Promega products.

Figures

The Create New Dye Set window.Figure 1. The Create New Dye Set window.

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The Calibration Run window.Figure 2. The Calibration Run window.

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