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CEQ-8000 Run Extraction 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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CEQ-8000 Run Extraction Manual

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    1. CEQ-8000 Run & Extraction Manual This easy-to-follow manual will guide you through every step of running and extracting your CEQ-8000 ® 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.

    3. Step 1 - Beckman CEQ8000 Start menu

    4. Fill in samples names in the appropriate rows. 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 Save Sample plate (on date), green rows become blue Step 2 – Fill in sample names

    5. Step 3 - Prepare sample plate CEQ separation buffer in Buffer tray (almost full) Mix 32 ul Formamide with 0,3 ul CEQ-600 marker (create mastermix, mix well) Divide 32 ul per well on separation tray Add 0,7 ul MLPA PCR sample per well Add mineral oil on top

    6. Click on Access Plates

    8. Step 6 - Open sample door & insert sample plates

    9. Start

    11. Click start run

    12. Step 10 - Wait for run… Continue after run with data exploration and extraction

    13. Step 11 – Start fragment analysis Start fragment analysis

    14. Step 12 – Create study from raw data

    15. Step 13 – Select sample data

    16. DATA to be analyzed Click Next Step 14 – Proceed with selected data

    17. Step 15 – Select analysis parameter set Select analysis parameter settings (recommended is 1% for data extraction). More peak filtering will occur in the Cofffalyser. Click Next

    18. Click Analyze for analysis of selected samples Step 16 – Analyze selected data

    19. Step 17 – Status of analyzed data Samples in green have been analyzed correctly

    20. Click finish to explore analyzed results Step 18 – Finish Analysis

    21. Double click to view a sample run Step 19 – Explore analyzed results

    22. Blue = Ran MLPA probes Red = ROX marker probes

    23. DESELECT D1, D2 AND D3, but NOT D4 RIGHT CLICK; COPY TO EXPORT IMAGE TO POWERPOINT Step 21 – Deselect other colors

    24. Return to fragment analysis list for data extraction Step 22 – Return to Fragment Analysis

    25. Select File, Export Fragments/ Genotypes (containing all files). You have now exported all sample runs. The resulting file is a CEQ project file. This file can later be imported in the Coffalyser. Step 23 – Export Results Sample runs

    26. Give your CEQ project file (of the exported sample data) a file name and save Step 24 – Data Export

    27. Results exportation Screen, after exportation click OK Step 25 – Save sample data

    28. PLACE the two CSV files on USB disk CSV files contain multiple sample runs and can directly be imported into the Coffalyser for MLPA analysis! Step 26 – Transferring data to Coffalyser

    29. 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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