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

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Determining T m Values The following table describes the elements of the Dissociation Plot: (continued) Component Description Plot drop-down list Chooses the data displayed within the plot based on the derivative calculation. The list offers the following selections: ♦ Raw – When selected, this option plots the normalized reporter fluorescence data (Rn ) on a graph of fluorescence vs. temperature (see below left). ♦ Derivative – When selected, this option plots derivative data (Rn ´) on a graph of the derivative vs. temperature (see below right). The derivative data is the negative of the rate of change in fluorescence as a function of temperature. The following figures show the plots accessible from the Plot drop-down list. Detector drop-down list Raw Plot Derivative Plot Chooses the data displayed within the plot based on detector name. To determine the T m value of a melting curve within the Dissociation Plot: Step Action 1 Move the mouse pointer over the green Tm line located on the Y-axis line of the plot. The mouse pointer becomes a hand. 2 Click and drag the Tm line to the maximum point of the derivative plot of interest. The SDS software displays the T m for the curve below the T m line. T m display and slider Note The apex of the curvature of represents the maximum rate of change in normalized fluorescence. Real-Time Analysis 6-23
After the Analysis Changing the Plate Document Display Settings Saving the Plate Document 6-24 Real-Time Analysis Before printing or exporting the analyzed data, the software allows you to reconfigure the appearance of several elements of the plate document including the results table, plate grid, and most plots. The software allows you to save any changes to the appearance of the plate document, however it does not save the threshold or baseline values made during the analysis. To save the plate document, select Save from the File menu. Printing a Report The SDS software can print a report of the analyzed data containing individual or multiple elements of the plate document. Exporting Plate Document Data To configure the display settings for the plate document: Step Action 1 From the View menu, select Display Settings. 2 From the Display Settings dialog box, click the help button ( instructions on modifying the display settings. ) for further To print a report of the plate document data: Step Action 1 From the File menu, select Print Report. 2 From the Print Report dialog box, click the help button ( setting up, previewing, and printing the report. ) for instructions on Exporting Plate Document Data as a Tab-Delimited Text File TheSDSsoftwarecanexportraworanalyzeddataintab-delimited(*.txt)formatforall or a select group of wells on a plate document. The exported files are compatible with most spreadsheet applications and programs that can read tab-delimited text. To export run data as a tab-delimited text file, choose one of the following for further instructions: ♦ See “Exporting Plate Document Data” on page B-9. ♦ Click the help button ( ) within the table view. Help button Exporting Plots as Graphics The SDS software can export most panes and plots of the plate document as JPEG (Joint Photographic Experts Group) graphic files. The JPEG file format is compatible with most word processing and spreadsheet applications and can be incorporated directly into HTML documents for viewing by most web browser software. To export a plot as a graphic file, see “Exporting Graphics” on page B-8 or click the help button ( ) within the plot of interest for further instructions.
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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
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
Page 86 and 87: To create plate documents from a te
Page 88 and 89: Adding Plates to the Plate Queue Re
Page 90 and 91: Loading Plates To load plates onto
Page 92 and 93: End-Point Analysis 5 In This Chapte
Page 94 and 95: Section: Allelic Discrimination In
Page 96 and 97: Algorithmic Manipulation of Raw All
Page 98 and 99: Before You Begin Using SDS Online H
Page 100 and 101: Analyzing a Completed Allelic Discr
Page 102 and 103: Calling Allele Types To call allele
Page 104 and 105: Scrutinizing the Allele Calls To an
Page 106: After the Analysis Changing the Pla
Page 109 and 110: Real-Time Runs on the 7900HT Instru
Page 111 and 112: Overview About Absolute Quantificat
Page 113 and 114: Before You Begin Using SDS Online H
Page 115 and 116: Analyzing the Run Data Configuring
Page 117 and 118: Setting the Baseline and Threshold
Page 119 and 120: Eliminating Outliers For any PCR, e
Page 121 and 122: Viewing the Standard Curve 6-14 Rea
Page 123 and 124: 6-16 Real-Time Analysis
Page 125 and 126: Overview About Dissociation Curve A
Page 127 and 128: Analysis Checklist WhereYouArein th
Page 129: Determining T m Values for the Anal
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
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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
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Calculating Threshold Cycles A-10 T
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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
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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
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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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