Applied Biosystems 7900HT Fast Real-Time PCR System and SDS ...

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Chapter 2Getting StartedTable 2-1Instrument Status LightsLight/Appearance Status Action(Red)SolidThe 7900HT instrument hasdetected a fatal problem.Power off the instrument, waitfor 30 sec, and then restart.Note: If the problem persists,contact Applied BiosystemsTechnical Support.2-6 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:38 am, CH_GetStart.fm
Using the SDS SoftwareUsing the SDS SoftwareStarting theSoftwareAbout theSoftwareInterface1. Do one of the following:• Select > Programs > Applied Biosystems > SDS 2.2.1 >SDS 2.2.1.• Double-click (SDS 2.2.1) on the computer desktop.If you are using an SDS Enterprise Database on your local area network, thesoftware will automatically prompt you to log in.2. (Database Only) In the Login dialog box, enter your user name and password,and click .Note: When working with a database, the SDS software requires that all usershave a user account and password (see the SDS Enterprise Database for theApplied Biosystems 7900HT Fast Real-Time PCR System Administrators Guide(PN 4351669) for more information on assigning and modifying user accounts.)The computer starts the SDS software and attempts to establish communication withthe 7900HT instrument. If the connection is successful, the software displays theConnected icon () in the status bar when a plate document is open.See “About the Message Bar” on page 2-9 for more information.All software operations and displayed information occur inside the workspace of theSDS software. The workspace provides quick access to all elements of the softwarethrough the menubar and a pair of toolbars. Figure 2-3 summarizes the features of theuser interface of the SDS software.MenubarContains a directory of menusgoverning the operation of thesoftwareWindow buttonsMinimize ( ), maximize ( ),or close ( ) the windowGeneral ToolbarContains icons for controllingthe basic functions of thesoftware (see page 2-8)Display ToolbarContains icons for controllingthe display of information inthe SDS software workspace(see page 2-8)Message BarDisplays messages that indicatethe status of the instrument andthe SDS software (see page 2-9)Figure 2-3Elements of the SDS Software User InterfaceInstrument Connection IconIndicates the status of theconnection to the 7900HTinstrument (see page 2-9)Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide 2-7DRAFTSeptember 1, 2004 11:38 am, CH_GetStart.fm
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Applied Biosystems7900HT Fast Real-
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ContentsPrefaceHow to Use This Guid
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Chapter 4Operating the InstrumentNo
Page 7 and 8: Chapter 7Maintaining the Instrument
Page 9 and 10: Appendix D Theory of OperationFluor
Page 11 and 12: PrefaceHow to Use This GuidePurpose
Page 13 and 14: Safety and EMC Compliance Informati
Page 15 and 16: Symbols on InstrumentsSymbols on In
Page 17 and 18: General Instrument SafetyGeneral In
Page 19 and 20: Chemical Waste SafetyChemical Safet
Page 21 and 22: Physical Hazard SafetyOvervoltageRa
Page 23 and 24: Workstation SafetyWorkstation Safet
Page 25 and 26: Product Overview 11In This Chapter
Page 27 and 28: 7900HT FAST Real-Time PCR SystemSec
Page 29 and 30: 7900HT InstrumentInterchangeableThe
Page 31 and 32: 7900HT FAST Real-Time PCR SystemBar
Page 33 and 34: Compatible ConsumablesCompatible Co
Page 35 and 36: Instrument ConnectionsFixed-Positio
Page 37 and 38: Section 1.2 Getting to Know the Sof
Page 39 and 40: SDS Software Related Files and Form
Page 41 and 42: 7900HT FAST Real-Time PCR SystemMan
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Page 45 and 46: Section 1.3 SDS Enterprise Database
Page 47 and 48: * + Enter* +Enter3Down UpNumLockSys
Page 49 and 50: About the SDS Enterprise Database S
Page 51 and 52: Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
Page 53 and 54: Getting Started 22In This Chapter G
Page 55 and 56: Getting StartedUsing the SDSSoftwar
Page 57: GR23967900HTPowering On the 7900HT
Page 61 and 62: Using the SDS SoftwareAbout theMess
Page 63 and 64: Basic Software Skills TutorialNotes
Page 65 and 66: Basic Software Skills TutorialExerc
Page 67 and 68: Basic Software Skills TutorialExpor
Page 73 and 74: Basic Software Skills TutorialLesso
Page 77 and 78: Basic Software Skills Tutorial3. Se
Page 81 and 82: Using SDS Plate DocumentsUsing SDS
Page 83 and 84: Using SDS Plate DocumentsWell Inspe
Page 85 and 86: Preparing a Run 33In This Chapter N
Page 87 and 88: Notes for Database UsersDescription
Page 89 and 90: Workflow OverviewWorkflow OverviewE
Page 91 and 92: Workflow OverviewAllelicDiscriminat
Page 93 and 94: Step 1 - Creating a Plate DocumentS
Page 95 and 96: Step 2 - Applying Detectors and Mar
Page 101 and 102: Step 3 - Configuring the Plate Docu
Page 103 and 104: Step 5 - Programming the Plate Docu
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Step 6 - Saving the Plate Document
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Step 7 - Creating a Plate Document
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Step 9 - Running the Plate on the 7
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Operating the Instrument 44In This
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Notes for Database UsersDescription
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Section 4.1 Consumable PreparationS
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Compatible ConsumablesTable 4-1Comp
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Preparing Optical Plates for Usea.
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Preparing TaqMan Low Density Arrays
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Section 4.2 Running an Individual P
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Running a Single Plate (Using the S
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Running a Single Plate (Using the S
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After the RunAfter the RunUser Acce
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Section 4.3 Automated OperationSect
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Operating the Software with an SDS
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Operating the Software without an S
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Running Plates Using the Automation
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Running Plates Using the Automation
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Analyzing End-Point Data 55In This
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Notes for Database UsersNotes for D
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Section 5.1 Allelic DiscriminationS
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OverviewTable 5-1Signal and Sequenc
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Before You BeginBefore You BeginUsi
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Opening the Run DataOpening the Run
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Calling and Scrutinizing Allelic Di
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After the AnalysisSaving theResults
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Analyzing Real-Time Data 66In This
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Section 6.1 Absolute Quantification
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OverviewAlgorithmicManipulation ofR
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Analysis ChecklistAnalysis Checklis
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Analyzing the DataAnalyzing the Dat
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Viewing ResultsViewing ResultsViewi
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Section 6.2 Relative Quantification
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OverviewAlgorithmic Manipulation of
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OverviewAutomatic Outlier RemovalAb
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Getting StartedGetting StartedUsing
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Options for Analyzing Relative Quan
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Creating the Studyd. In the Plate Q
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Analyzing the Study• Manual Ct -
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Analyzing the StudySpecifying the A
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Viewing ResultsViewing ResultsDispl
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Viewing ResultsAbout DownArrowsDown
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After the AnalysisAfter the Analysi
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Section 6.3 Dissociation Curve Anal
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Before You BeginExample ResultsFigu
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Opening the Run DataOpening the Run
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Determining T m Values for the Anal
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Section 6.4 Procedure ReferenceSect
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Setting the Baseline and Threshold
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Eliminating Outlying AmplificationE
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Eliminating Outlying Amplification6
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After the AnalysisSaving theResults
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Maintaining the Instrument 77In Thi
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Section 7.1 Maintaining the 7900HT
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Replacing the Sample BlockMaterials
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Replacing the Sample Block9. Loosen
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7900HT FAST Real-Time PCR SystemRep
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Changing the Plate Adapter4. Place
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Decontaminating the Sample BlockCle
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Performing a Background RunPreparin
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Performing a Background RunAnalyzin
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Performing a Pure Dye RunAfter a ru
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Performing a Pure Dye Run• Fast 9
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Performing a Pure Dye RunAnalyzing
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Adding Custom Dyes to the Pure Dye
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Adding Custom Dyes to the Pure Dye
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Verifying Instrument PerformanceTab
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Verifying Instrument PerformancePre
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Section 7.2 Maintaining the Plate H
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Adjusting the Sensitivity of the Pl
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Adjusting the Sensitivity of the Pl
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7900HT FAST Real-Time PCR SystemAli
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Aligning the Plate Handler5. Using
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Aligning the Plate Handler7. Using
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Aligning the Plate Handler13. Click
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7900HT FAST Real-Time PCR SystemAli
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Aligning the Fixed-Position Bar Cod
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Section 7.3 Maintaining the Compute
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Maintaining the SDS softwareSeveral
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Troubleshooting 88In This Chapter T
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Troubleshooting TableTable 8-1Troub
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Low Precision or IrreproducibilityL
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Low Precision or IrreproducibilityD
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Background RunsBackground RunsBackg
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Pure Dye Runs6. Repeat step 4 until
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End-Point Runs (Allelic Discriminat
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Software and 7900HT InstrumentTable
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Zymark Twister Microplate Handler a
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TaqMan Low Density ArrayTable 8-6Tr
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Software ReferenceAAIn This Appendi
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Importing Plate Document Setup Tabl
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Setup Table Files1. File VersionDes
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Setup Table Files6. Detectors ListD
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Setup Table Files9. Markers List (A
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Setup Table FilesFormat(for a singl
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Setup Table FilesFormat(for a singl
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Setup Table FilesExample Code A-16A
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Exporting Plate Document Data4. In
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Operating the SDS Software from a C
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Using the Search ToolLogical Operat
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Connecting SDS Software to the Data
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Designing TaqMan Reagent-BasedAssay
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Assay Development Guidelines• For
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Design Tips for Allelic Discriminat
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Kits, Reagents, and ConsumablesCCIn
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Consumables and DisposablesConsumab
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Instrument Maintenance and Verifica
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Custom Oligonucleotide SynthesisTab
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Theory of OperationDDIn This Append
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Fluorescent-Based ChemistriesBasics
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Real-Time Data AnalysisPhase 2: Lin
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Real-Time Data AnalysisSignificance
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A similar equation for the endogeno
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Limited Warranty StatementEEWarrant
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BibliographyGeneral Paperson TaqMan
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Klein, D., Janda, P., Steinborn, R.
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Dolken, L., F. , Schuler, and G. ,
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AllelicDiscriminationVirtanen M., H
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Glossary.sdd.sdm.sds.sdt∆C T∆
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ackgroundbaselinecalibratorcDNA(com
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minor groovebinder (MGB)multicompon
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R nrunsessionsingle nucleotidepolym
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IndexSymbols- 6-31↑ 6-33Numerics7
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fluorescent, common sources 8-7isol
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adjusting step parameters 3-21confi
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sample block locking bar 7-8sample
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Worldwide Sales and SupportApplied
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