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GeneMapper RunExtraction Manual

How to use the Coffalyser manuals. If you are a first-time user, please start with the Excel-Coffalyser Preparation Manual, followed by the Quick Analysis Manual and the appropriate Run

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GeneMapper RunExtraction Manual

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    1. GeneMapper Run&Extraction Manual This easy-to-follow manual will guide you through every step of running and extracting your GeneMapper® files into the Coffalyser program. Make sure you first read the Coffalyser-Excel Preparation Manual!

    2. How to use the Coffalyser manuals If you are a first-time user, please start with the Excel-Coffalyser Preparation Manual, followed by the Quick Analysis Manual and the appropriate Run&Extraction Manual (if applicable). Note that you only need the Run&Extraction Manuals if you wish to use the data filtering function of the Coffalyser. In contrast, if you’re already using a filtering system of another program and have raw filtered peak heights/areas, there is no need to follow the Run&Extraction manual. This pre-filtered data can simply be imported, as is explained in the Extensive Analysis Manual. FSA files coming from an ABI3130 or 3730 cannot be used for direct import. Therefore, they always need to be size-called in GeneMapper first, as is described in this manual.

    3. Step 1 - Run Protocol on F.D.C. V3 Start Foundation Data Collection Version 3.0 Select Plate Manager Select New Fill in: Name: fill in the plate name (data will be stored in folder under that name) Application: GeneMapper-pa-pc310 Owner Name Operator Name: fill in your name (click ok)

    4. Step 2 - Plate Editor Screen Fill in samples names Tip: the same names will be imported by the Coffalyser, so choose names that ensure a clear identification throughout the whole data analysis process!! For methylation analysis, give undigested & digested samples identical names e.g. sample1_digested & sample1_undigested Priority: 100 (pops up automatically) Sample Type: Sample Size Standard: Used standard (GS-500 or GS-600) Panel: None (unless made) Analysis Method: Micro satellite Default Result Group 1: ?? Instrument Protocol 1: depends on gel (FA36-POP7-D) Do not fill in rest of options! Edit: Fill down for rest of samples (click ok)

    5. Step 3 - Run Scheduler Select plate view Click Find All Put plate in machine (press tray and wait for tray to appear on the screen) Click on plate name and on grid once Start run (in plate view, click green play button)

    6. Step 4 - Plate View Be careful never to touch the capillaries! Check the order of the samples When asked, click ok In instrument status: check if machine starts

    7. Step 6 - Log in Log in to Genemapper

    8. Step 7 - Starting New Analysis File ? new project Microsatellite ? click ok

    9. Step 8 - Adding New Samples In Select File ? select Add Samples to Project Select all files ? click Add to list ? click Add

    10. Step 9 - Analyze Samples Click on Analyze (click green play button) When asked, fill in your name in and click ok

    11. Step 10 - Select All Runs The simplest way to streamline your analysis to the Coffalyser Analysis macro is to export all your Reference Runs to one File and all your Sample Runs to another file Select All your reference runs and select Display Plots Repeat the next steps for your Sample runs!

    12. Step 11 - Exporting Data Tables All selected runs will be displayed underneath each other Deselect all other Labels except for FAM (blue) The displayed table should contain ONLY the following columns, respectively: Dye/sample peak; Sample File name; Size; Height; Area; Data Point. If this is not the case ? see next slide! Now Select File, Export Table The exported Reference and Sample Run tables can be imported in the Coffalyser as GeneMapper project files

    13. Step 12 - Changing Table contents It is very important that only these six columns are selected: 1. Dye/sample peak 2. Sample File name 5. Size 6. Height 7. Area 8. Data Point To change the Table contents, click on Tools; Plot Settings Now select these 6 columns only. If this is not done correctly, the data transfer to the Coffalyser won’t work!! You can now proceed with the Coffalyser Quick Analysis Manual, available from the Coffalyser-section on our website www.mlpa.com.

    14. Further help needed? The following word & ppt presentations are available for help on the Coffalyser: MLPA Copy Number Protocol MLPA Fragment Analysis Protocol MLPA Data Analysis Protocol Coffalyser/Excel Preparation Manual (this manual) Run & Extraction Manual for GeneMapper ® Run & Extraction Manual for GeneScan ® Run & Extraction Manual Beckman CEQ8000 ® Run & Extraction Manual Peak Scanner Software ® About the Coffalyser Method For more information on data analysis, visit our website www.mlpa.com For data analysis questions, contact info@mlpa.com

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