ABI Prism® 7900HT Sequence Detection System ... - OpenWetWare

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Using the SDS Software Online Help For More Information About This Manual The SDS software features an online help system that can guide you through the procedures for setting up, performing, and analyzing runs. To get help at any time, click a Help button located within the dialog box or window in which you are working. The SDS software provides two ways to access the online help as follows: For information about the ABI PRISM 7900HT Sequence Detection System or the SDS software, Applied Biosystems recommends the following references: Intended Audience This guide is written for technicians, scientists, and researchers who will use ABI PRISM 7900HT Sequence Detection System (SDS) instruments. Background Needed This manual assumes that you are familiar with the following: ♦ Basic Microsoft® Windows® operations such as using the mouse, choosing commands, working with windows, and using the hierarchical file system ♦ A general understanding of electronic storage devices and data files ♦ An understanding of assay preparation and basic laboratory techniques Computer Vocabulary and Operations To… Then… access general help select SDS Online Help from the Help menu. get help for using a specific click a help button ( ) located within the dialog box or dialog box, plot, or feature window in which you are working. Title P/N ABI PRISM 7900HT Sequence Detection System Site Preparation and Safety Guide 4317595 ABI PRISM 7900HT Sequence Detection System Software Online Help — Microsoft Windows Operating System Online Help — To use the ABI PRISM 7900HT Sequence Detection System, you should be familiar with the following basic computer vocabulary and operations: Vocabulary and Operations Description Using the mouse Clicking and double-clicking, selecting, and dragging. Choosing commands Using menus and drop-down lists, dialog boxes, radio buttons, and check boxes. Working with windows Opening and closing, resizing and repositioning, scrolling, understanding the active window. Using the Microsoft Windows hierarchical file system Finding files and creating folders. Getting Started 3-3
Conventions Used in This Manual How This Manual is Organized 3-4 Getting Started This manual uses the following conventions to convey information: Convention Definition Examples > This symbol is used to convey a command or directory path in the Windows operating system. Bold text Bold text appearing with procedures corresponds to the text as it appears on the screen. ♦ From the Start menu, select Programs > SDS 2.0 > SDS 2.0. ♦ Navigate to the Program Files > Applied Biosystems > SDS 2.0 > Templates directory. ♦ From the File menu, select Save. ♦ The Detector Manager dialog box opens. This manual contains the following chapters and supporting appendices: Chapter/Appendix Content 1 Safety Explains information on ABI PRISM 7900HT Sequence Detection System safety 2 Product Overview Describes the components of the ABI PRISM 7900HT Sequence Detection System and its software 3 Getting Started Introduces and explains how to use this manual and the SDS software 4 Run Setup and Basic Operation Explains how to create and run plate documents on the ABI PRISM 7900HT Sequence Detection System 5 End-Point Analysis Describes how to analyze data from allelic discrimination experiments 6 Real-Time Analysis Describes how to analyze data from absolute quantification and dissociation curve experiments 7 System Maintenance Explains how to perform both routine and incidental system maintenance for the components of the ABI PRISM 7900HT Sequence Detection System 8 Troubleshooting Contains tips for troubleshooting problems with the ABI PRISM 7900HT Sequence Detection System 9 User Bulletins This chapter is reserved for user bulletins A Theory of Operation Describes the principles behind the operation of the ABI PRISM 7900HT Sequence Detection System B Importing and Exporting Plate Document Data Explains the Import/Export function of the SDS software and also diagrams the structure and annotation of setup table files C Designing TaqMan Assays Contains brief instructions for designing TaqMan probe and Sequence Detection primer sets D Kits, Reagents and Consumables Contains a list of Applied Biosystems kits and consumables for use with the 7900HT instrument E References Contains a bibliography of references for this manual F Contacting Technical Support How to contact Applied Biosystems Technical Support G Limited Warranty Statement The Applied Biosystems limited warranty statement
Page 1 and 2: ABI PRISM ® 7900HT Sequence Detect
Page 3 and 4: © Copyright 2001, Applied Biosyste
Page 5 and 6: iv Section:PlateDocumentSetup......
Page 7 and 8: vi A Theory of Operation Fluorescen
Page 9 and 10: Attention Words and Warning Labels
Page 11 and 12: About Waste Profiles A waste profil
Page 13 and 14: Safe Instrument Use Before Operatin
Page 16 and 17: Product Overview 2 In This Chapter
Page 18 and 19: Section: Getting to Know the Hardwa
Page 20 and 21: Interchangeable Thermal Cycler Bloc
Page 22 and 23: Computer Description The computer c
Page 24 and 25: Zymark Twister Microplate Handler D
Page 26 and 27: Instrument Connections Electrical C
Page 28 and 29: Section: Getting to Know the Softwa
Page 30 and 31: Managing Sequence Detection System
Page 32 and 33: Getting Started 3 In This Chapter T
Page 36 and 37: Turning on the ABI PRISM 7900HT Seq
Page 38 and 39: Using the SDS Software Workspace La
Page 40 and 41: Using the General Toolbar Using the
Page 42 and 43: Basic Software Skills Tutorial Abou
Page 44 and 45: Exercise 3: Opening a Plate Documen
Page 46 and 47: Lesson 2: Viewing and Resizing Pane
Page 48 and 49: Exercise 2: Selecting Multiple Well
Page 50 and 51: Lesson 4: Using the Hand-Held Bar C
Page 52 and 53: Using SDS Plate Documents Using Mul
Page 54 and 55: Run Setup and Basic Operation 4 In
Page 56 and 57: Setup Checklists Experiments/Runs P
Page 58 and 59: Section: Plate Document Setup In Th
Page 60 and 61: Step 2 - Applying Detectors and Mar
Page 62 and 63: Creating an Allelic Discrimination
Page 64 and 65: Step 3 - Configuring the Plate Docu
Page 66 and 67: Step 4 - Programming the Plate Docu
Page 68 and 69: To create a method for the absolute
Page 70 and 71: Step 5 - Saving the Plate Document
Page 72 and 73: Step 7 - Applying Sample and Plate
Page 74 and 75: Section: Running an Individual Plat
Page 76 and 77: Preparing and Running a Single Plat
Page 78 and 79: Operating the 7900HT Instrument Usi
Page 80 and 81: After the Run Analyzing the Run Dat
Page 82 and 83: Section: Running Multiple Plates Us
Page 84 and 85:
Adding a Plate Document to the Plat
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To create plate documents from a te
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Adding Plates to the Plate Queue Re
Page 90 and 91:
Loading Plates To load plates onto
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End-Point Analysis 5 In This Chapte
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Section: Allelic Discrimination In
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Algorithmic Manipulation of Raw All
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Before You Begin Using SDS Online H
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Analyzing a Completed Allelic Discr
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Calling Allele Types To call allele
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Scrutinizing the Allele Calls To an
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After the Analysis Changing the Pla
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Real-Time Runs on the 7900HT Instru
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Overview About Absolute Quantificat
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Before You Begin Using SDS Online H
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Analyzing the Run Data Configuring
Page 117 and 118:
Setting the Baseline and Threshold
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Eliminating Outliers For any PCR, e
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Viewing the Standard Curve 6-14 Rea
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6-16 Real-Time Analysis
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Overview About Dissociation Curve A
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Analysis Checklist WhereYouArein th
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Determining T m Values for the Anal
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After the Analysis Changing the Pla
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Recommended Maintenance Schedule Ma
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Replacing the Sample Block When to
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7-6 System Maintenance To remove th
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7-8 System Maintenance To replace t
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7-10 System Maintenance To replace
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Cleaning the Sample Block Wells 7-1
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Prepare a Background Plate Document
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Extracting the Background 7-16 Syst
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Materials Required The following ma
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Extracting Pure Dye Information fro
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Constructing a Custom Pure Dye Plat
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Verifying Instrument Performance Us
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Preparing and Running an RNase P Pl
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Adjusting the Sensitivity of the Pl
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Testing the Adjustment 7-30 System
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Aligning the Plate Handler When to
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7-34 System Maintenance To align th
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Re-checking the Input Stack 1 7-36
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Defining the Positions of the Remai
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Aligning the Fixed-Position Bar Cod
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7-42 System Maintenance To position
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7-44 System Maintenance
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General Computer Maintenance Mainte
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Maintaining the SDS software Admini
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Troubleshooting Table 8-2 Troublesh
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Low Precision or Irreproducibility
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Writing on the Reaction Plates Fluo
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Background Runs Background Troubles
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Pure Dye Runs Pure Dye Troubleshoot
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8-12 Troubleshooting Troubleshootin
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Software and 7900HT Instrument Trou
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8-16 Troubleshooting Troubleshootin
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User Bulletins 9 9 About This Chapt
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Fluorescent-Based Chemistries Funda
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Fluorescence Detection and Data Col
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Normalization of Reporter Signals A
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Determining Initial Template Concen
Page 209 and 210:
Calculating Threshold Cycles A-10 T
Page 212 and 213:
Importing and Exporting Plate Docum
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Configuring the Setup Table File wi
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About the Setup Table File Format S
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Setup Table Elements (continued) Nu
Page 220 and 221:
Exporting Plate Document Data Expor
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Designing TaqMan Assays C In This A
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Design Probes and Primers The follo
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Design Tips for Allelic Discriminat
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Kits, Reagents and Consumables D In
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Consumables and Disposables The ABI
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TaqMan Pre-Developed Assays and Rea
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Contacting Technical Support F Serv
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G-2 Limited Warranty Statement No a
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A(continued) Automation Controller
Page 243 and 244:
I(continued) installing plate adapt
Page 245 and 246:
Q quantifying probes and primers C-
Page 248 and 249:
Headquarters 850 Lincoln Centre Dri
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