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Methyl Primer Express ® Software Version 1.0 Getting Started Guide
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Methyl Primer Express ® Software Getting Started Guide Getting Started Analyzing Your gDNA Sequence Designing Primers
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© Copyright 2006, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF. DISCLAIMER OF LICENSE: Use of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly or by estoppel. TRADEMARKS: AB (Design), Applied Biosystems, and Primer Express are registered trademarks and Applera and Celera Genomics are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. All other trademarks are the sole property of their respective owners. Part Number 4370961 Rev. A 04/2006
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Contents v Methyl Primer Express ® Software v1.0 Getting Started Guide Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x Chapter 1 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 About Methyl Primer Express ® Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 About DNA Methylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 About the Example Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Using This Guide with Your Own Sequence Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Chapter 2 Analyzing Your gDNA Sequence. . . . . . . . . . . . . . . . . 5 Workflow Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Starting Methyl Primer Express ® Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Example Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Importing a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Annotating the Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Finding CpG Islands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Reviewing the CpG Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Selecting a Target Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Reviewing the DNA Sequence Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Designing Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Optional Ways to Annotate a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Naming Your Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Annotating the Sequence with the Transcription Start Point . . . . . . . . . . . . . . . 14 Annotating the Sequence with the Translation Start Codon . . . . . . . . . . . . . . . . 15
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vi Methyl Primer Express ® Software v1.0 Getting Started Guide Contents Chapter 3 Designing Primers. . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Designing Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Guidelines for Selecting a Primer Pair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Example Workflow (Continued) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Selecting Primer Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Designing BSP Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Selecting a Primer Pair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Creating the BSP Primer Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Recommendations for Designing Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Recommendations for Bisulfite Sequencing (BSP) . . . . . . . . . . . . . . . . . . . . . . 26 Recommendations for Methylation-Specific PCR (MSP) . . . . . . . . . . . . . . . . . . 26
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vii Methyl Primer Express ® Software v1.0 Getting Started Guide Preface How to Use This Guide
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