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

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Table 8-1 Troubleshooting Table (continued) Category Symptom Page Instrument and Automation Module Problems Software and 7900HT Instrument Zymark Twister Microplate Handler and Fixed-Position Bar Code Reader SDS software will not launch Software crashes/freezes the computer or displays an error message Communication error Thermal cycler errors Automation Controller Software cannot find a plate document file Computer and/or software displays the Run Completed Successfully dialog box but will not respond and appears to be frozen Run will not start Computer is slow when analyzing data, opening or closing dialog boxes, and other software processes. The computer will not logon to the Windows Operating System. The computer will not boot up at all. Plate handler emits grinding noise when picking up or putting down plates Plate handler arm contacts racks when retrieving or stacking plates Plate handler arm releases plates awkwardly into the plate stack Reaction plates tip or tilt when placed into the instrument tray by the plate handler arm Plate handler fails to sense or grasp plates Plates stick to the gripper fingers of the plate handler arm Plate handler does not restack plates in original locations Fixed-position bar code reader not reading plate bar codes 8-14 8-17 Troubleshooting 8-3
Low Precision or Irreproducibility Improper Threshold Setting 8-4 Troubleshooting Overview There are many reasons why an assay run with the ABI PRISM 7900HT Sequence Detection System can have less than optimal precision. Factors that can affect precision are described in detail below. Factor See Page Improper Threshold Setting 8-4 Imprecise Pipetting 8-5 Non-Optimized Chemistry 8-5 Incomplete Mixing 8-5 Air Bubbles 8-5 Splashing PCR Reagents 8-5 Drops 8-6 Writing on the Reaction Plates 8-6 Fluorescent Contamination on the Plates 8-6 Errors 8-6 Contaminated Sample Block 8-7 Improper or Damaged Plastics 8-7 Low Copy Templates 8-7 Use of Non-Applied Biosystems PCR Reagents 8-7 The key to high-precision quantitative PCR is accurate detection of the geometric phase. The ABI PRISM 7900HT Sequence Detection System typically delivers sufficient sensitivity so that at least 3 cycles of the geometric phase are visible, assuming reasonably optimized PCR conditions. The SDS software calculates a fixed signal intensity, called a threshold, which each signal generated from PCR amplification must reach before it is recognized as actual amplification. The calculated threshold is an approximation, and should be examined and modified as needed. Modifying the Threshold In a real-time document of the SDS software, the threshold can be modified via the Amplification Plot view following analysis of the run data. See “Setting the Baseline and Threshold Values for the Run” on page 6-10 for more information.
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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
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Analysis Checklist WhereYouArein th
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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 and 178: General Computer Maintenance Mainte
Page 179 and 180: Maintaining the SDS software Admini
Page 181: Troubleshooting Table 8-2 Troublesh
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
Page 228 and 229: Kits, Reagents and Consumables D In
Page 230 and 231: 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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