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

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Shi M.M., S.P. Myrand, M.R. Bleavins and F.A. de la Iglesia. High-throughputgenotyping method for glutathione S-transferase T1 and M1 gene deletions usingTaqMan probes. Res. Commun. Mol. Pathol. Pharmacol. 103:3-15, 1999.Bibliography-8 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:38 am, Bibliography.fm
Glossary.sdd.sdm.sds.sdt∆C T∆∆C T∆R nThe file extension of an ABI PRISM SDS Detector file for SDS software for the7900HT instrument.The file extension of a SDS 7900HT Multiple Plate Document (*.sdm) for SDSsoftware for the 7900HT instrument.The file extension of a SDS 7900HT Document (*.sds) for SDS software for the7900HT instrument.The file extension of a SDS 7900HT Template Document (*.sdt) for SDS software forthe 7900HT instrument.The difference between the threshold cycle of a sample assay and the threshold cycleof the corresponding endogenous reference: ∆C T = C T (target) - C T - C T (endogenouscontrol).For a given cDNA target, the difference between the average ∆C T value of a targetsample and the average ∆C T for the corresponding calibrator sample:∆∆C T (test sample) = Avg∆C T (test sample) - Avg∆C T (calibrator sample). This valueis used to calculate expression fold value by the equation: Expression fold value =2 −∆∆C TThe normalized reporter signal minus the baseline signal. The baseline is establishedin the first few cycles of PCR. Like R n , ∆R n is not a fixed value but increases duringPCR when the amplicon copy number increases until the reaction approaches aplateau.5′ nuclease assay The 5′ (five prime) nuclease assay in combination with the TaqMan ® probes serves asthe basis for real-time polymerase chain reaction (PCR) technology on the 7900HTinstrument. See “Fundamentals of the 5´ Nuclease Assay” on page D-2 for a detaileddescription of the reaction.ABI PRISM SDSDetector file (*.sdd)SDS 7900HTMultiple PlateDocument (*.sdm)The SDS detector file is a tab-delimited flat file that is used to transfer detectorinformation to and from the SDS software using the Export and Import functions ofthe Detector Manager software. The file contains: (a) a header“SDS2.2.1[GDF[Global Detector File”, (b) tab-delimited data for each detector (alleleName, the name of the reporter dye, the name of the quencher dye, a description, acomment, the owner, the creation date and time, the modification date and time, andthe color used to code the detector in graphical displays of the SDS software).Multiple plate documents are used for the analysis of relative quantification data.Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide Glossary-1DRAFTSeptember 1, 2004 11:39 am, Glossary.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
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Chapter 7Maintaining the Instrument
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Appendix D Theory of OperationFluor
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PrefaceHow to Use This GuidePurpose
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Safety and EMC Compliance Informati
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Symbols on InstrumentsSymbols on In
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General Instrument SafetyGeneral In
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Chemical Waste SafetyChemical Safet
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Physical Hazard SafetyOvervoltageRa
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Workstation SafetyWorkstation Safet
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Product Overview 11In This Chapter
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7900HT FAST Real-Time PCR SystemSec
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7900HT InstrumentInterchangeableThe
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7900HT FAST Real-Time PCR SystemBar
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Compatible ConsumablesCompatible Co
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Instrument ConnectionsFixed-Positio
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Section 1.2 Getting to Know the Sof
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SDS Software Related Files and Form
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7900HT FAST Real-Time PCR SystemMan
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Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
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Section 1.3 SDS Enterprise Database
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* + Enter* +Enter3Down UpNumLockSys
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About the SDS Enterprise Database S
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Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
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Getting Started 22In This Chapter G
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Getting StartedUsing the SDSSoftwar
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GR23967900HTPowering On the 7900HT
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Using the SDS SoftwareUsing the SDS
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Using the SDS SoftwareAbout theMess
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Basic Software Skills TutorialNotes
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Basic Software Skills TutorialExerc
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Basic Software Skills TutorialExpor
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Basic Software Skills TutorialLesso
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Basic Software Skills Tutorial3. Se
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Using SDS Plate DocumentsUsing SDS
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Using SDS Plate DocumentsWell Inspe
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Preparing a Run 33In This Chapter N
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Notes for Database UsersDescription
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Workflow OverviewWorkflow OverviewE
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Workflow OverviewAllelicDiscriminat
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Step 1 - Creating a Plate DocumentS
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Step 2 - Applying Detectors and Mar
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Step 3 - Configuring the Plate Docu
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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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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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Page 325 and 326: Exporting Plate Document Data4. In
Page 327 and 328: Operating the SDS Software from a C
Page 329 and 330: Using the Search ToolLogical Operat
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Page 333 and 334: Designing TaqMan Reagent-BasedAssay
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Page 341 and 342: Consumables and DisposablesConsumab
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Page 349 and 350: Fluorescent-Based ChemistriesBasics
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Page 353 and 354: Real-Time Data AnalysisSignificance
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Page 359 and 360: BibliographyGeneral Paperson TaqMan
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Page 365: AllelicDiscriminationVirtanen M., H
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Page 377 and 378: fluorescent, common sources 8-7isol
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Page 384: Worldwide Sales and SupportApplied
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