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

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Defragmenting the Hard Drive Upgrading the Operating System Software Applied Biosystems recommends defragmenting the hard drive of the computer attached to the instrument at least once every week or before fragmentation reaches 10%. As the ABI PRISM 7900HT Sequence Detection System is used and files are deleted and created, the free space on the computer hard drive eventually is split into increasingly smaller blocks (called “clusters”). Consequently, as the SDS software creates new files and extends old ones, the computer cannot store each file in a single block. Instead, the system will ‘fragment’ the files by scattering their component pieces across different sectors of the hard drive. The fragmentation of SDS files decreases the performance of both the SDS software and the computer operating system. As the hard drive becomes fragmented, programs take greater time to access files because they must perform multiple seek operations to access the fragments. Several commercially available software utilities are available for repairing fragmented file systems. The software utility defragments broken files by combining their component pieces at a single location on the hard drive, thereby optimizing system performance. Do not upgrade the operating system of the computer connected to the 7900HT instrument unless instructed to do otherwise by an Applied Biosystems service engineer. New versions of the Microsoft Windows operating system can be incompatible with the SDS software and render it and the instrument inoperable. The Applied Biosystems service engineer maintains the operating system software as part of planned maintenance visits. During the visit, the engineer will update the computer operating system as upgrades become available and are validated by Applied Biosystems. System Maintenance 7-47
Maintaining the SDS software Administration Privileges Upgrading the 7900HT SDS Software Reinstalling the Software 7-48 System Maintenance IMPORTANT You must have administrator privileges on the computer to install and/or upgrade the SDS software. Applied Biosystems continually develops the SDS software to provide increased functionality and reliability of the ABI PRISM 7900HT Sequence Detection System. As updates become available, Applied Biosystems sends notifications of the upgrades to all ABI PRISM 7900HT Sequence Detection System customers. If an upgrade is user-installable, it can be found on the Applied Biosystems company Web site (see Appendix F, “Contacting Technical Support,” to visit the Applied Biosystems Web Site). Note Applied Biosystems service engineers perform regular updates the SDS software during planned maintenance visits. On rare occasions, when a piece of the SDS software becomes corrupt, it may be necessary to re-install the software. In the event that the software must be re-installed, observe the following guidelines to re-install or upgrade the software. ♦ Unless instructed to do otherwise, remove the SDS software using the uninstall utility. Do not delete the program folder from the Program Files directory. ♦ Install the SDS software under a user login that has administrator privileges on the computer. ♦ Unless instructed to do otherwise, re-install the SDS software to the same directory as the previous installation. ♦ Review all documentation accompanying the new software (such as installation notes or user bulletin). The updated version of the software may contain new features that require special consideration.
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ABI PRISM ® 7900HT Sequence Detect
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© Copyright 2001, Applied Biosyste
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iv Section:PlateDocumentSetup......
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vi A Theory of Operation Fluorescen
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Attention Words and Warning Labels
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About Waste Profiles A waste profil
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Safe Instrument Use Before Operatin
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Product Overview 2 In This Chapter
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Section: Getting to Know the Hardwa
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Interchangeable Thermal Cycler Bloc
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Computer Description The computer c
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Zymark Twister Microplate Handler D
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Instrument Connections Electrical C
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Section: Getting to Know the Softwa
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Managing Sequence Detection System
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Getting Started 3 In This Chapter T
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Using the SDS Software Online Help
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Turning on the ABI PRISM 7900HT Seq
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Using the SDS Software Workspace La
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Using the General Toolbar Using the
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Basic Software Skills Tutorial Abou
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Exercise 3: Opening a Plate Documen
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Lesson 2: Viewing and Resizing Pane
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Exercise 2: Selecting Multiple Well
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Lesson 4: Using the Hand-Held Bar C
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Using SDS Plate Documents Using Mul
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Run Setup and Basic Operation 4 In
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Setup Checklists Experiments/Runs P
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Section: Plate Document Setup In Th
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Step 2 - Applying Detectors and Mar
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Creating an Allelic Discrimination
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Step 3 - Configuring the Plate Docu
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Step 4 - Programming the Plate Docu
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To create a method for the absolute
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Step 5 - Saving the Plate Document
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Step 7 - Applying Sample and Plate
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Section: Running an Individual Plat
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Preparing and Running a Single Plat
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Operating the 7900HT Instrument Usi
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After the Run Analyzing the Run Dat
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Section: Running Multiple Plates Us
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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
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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
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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
Page 127 and 128: Analysis Checklist WhereYouArein th
Page 129 and 130: Determining T m Values for the Anal
Page 131 and 132: After the Analysis Changing the Pla
Page 133 and 134: Recommended Maintenance Schedule Ma
Page 135 and 136: Replacing the Sample Block When to
Page 137 and 138: 7-6 System Maintenance To remove th
Page 139 and 140: 7-8 System Maintenance To replace t
Page 141 and 142: 7-10 System Maintenance To replace
Page 143 and 144: Cleaning the Sample Block Wells 7-1
Page 145 and 146: Prepare a Background Plate Document
Page 147 and 148: Extracting the Background 7-16 Syst
Page 149 and 150: Materials Required The following ma
Page 151 and 152: Extracting Pure Dye Information fro
Page 153 and 154: Constructing a Custom Pure Dye Plat
Page 155 and 156: Verifying Instrument Performance Us
Page 157 and 158: Preparing and Running an RNase P Pl
Page 159 and 160: Adjusting the Sensitivity of the Pl
Page 161 and 162: Testing the Adjustment 7-30 System
Page 163 and 164: Aligning the Plate Handler When to
Page 165 and 166: 7-34 System Maintenance To align th
Page 167 and 168: Re-checking the Input Stack 1 7-36
Page 169 and 170: Defining the Positions of the Remai
Page 171 and 172: Aligning the Fixed-Position Bar Cod
Page 173 and 174: 7-42 System Maintenance To position
Page 175 and 176: 7-44 System Maintenance
Page 177: General Computer Maintenance Mainte
Page 181 and 182: Troubleshooting Table 8-2 Troublesh
Page 183 and 184: Low Precision or Irreproducibility
Page 185 and 186: Writing on the Reaction Plates Fluo
Page 187 and 188: Background Runs Background Troubles
Page 189 and 190: Pure Dye Runs Pure Dye Troubleshoot
Page 191 and 192: 8-12 Troubleshooting Troubleshootin
Page 193 and 194: Software and 7900HT Instrument Trou
Page 195 and 196: 8-16 Troubleshooting Troubleshootin
Page 198: User Bulletins 9 9 About This Chapt
Page 201 and 202: Fluorescent-Based Chemistries Funda
Page 203 and 204: Fluorescence Detection and Data Col
Page 205 and 206: Normalization of Reporter Signals A
Page 207 and 208: Determining Initial Template Concen
Page 209 and 210: Calculating Threshold Cycles A-10 T
Page 212 and 213: Importing and Exporting Plate Docum
Page 214 and 215: Configuring the Setup Table File wi
Page 216 and 217: About the Setup Table File Format S
Page 218 and 219: Setup Table Elements (continued) Nu
Page 220 and 221: Exporting Plate Document Data Expor
Page 222 and 223: Designing TaqMan Assays C In This A
Page 224 and 225: Design Probes and Primers The follo
Page 226 and 227: 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
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I(continued) installing plate adapt
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Q quantifying probes and primers C-
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Headquarters 850 Lincoln Centre Dri
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