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

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Appendix ELimited Warranty StatementThis Warranty is limited to the original location of installation and is not transferable.THIS WARRANTY IS THE SOLE AND EXCLUSIVE WARRANTY AS TO THEINSTRUMENT AND IS IN LIEU OF ANY OTHER EXPRESS OR IMPLIEDWARRANTIES, INCLUDING, WITHOUT LIMITATION, ANY IMPLIEDWARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULARPURPOSE AND IS IN LIEU OF ANY OTHER OBLIGATION ON THE PART OFAPPLIED BIOSYSTEMS.E-2 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:38 am, App_Warranty.fm
BibliographyGeneral Paperson TaqMan ®Reagents andNucleic AcidPreparationsBloch, W. 1991. A biochemical perspective of the polymerase chain reaction.Biochemistry 30:2735–2747.Förster, V. Th., 1948, Zwischenmolekulare Energie-wanderung und Fluoreszenz.Annals of Physics (Leipzig) 2: 55-75.Higuchi, R., Dollinger, G., Walsh, P.S., and Griffith, R. 1992. Simultaneousamplification and detection of specific DNA sequences. BioTechnology 10:413-417.Higuchi, R., Fockler, C., Dollinger, G. and Watson, R. 1993. Kinetic PCR analysis:Real-time monitoring of DNA amplification reactions. BioTechnology11:1026-1030.Lakowicz, J.R. 1983. Chapter 10. Energy Transfer. In: Principles of FluorescentSpectroscopy, Plenum Press, N.Y. pp, 303-339.Lee, L.G., Connell, C.R., and Bloch, W. 1993. Allelic discrimination bynick-translation PCR with fluorogenic probes. Nucl. Acids Res. 21: 3761-3766.Livak, K.J., Flood, S.J.A., Marmaro, J., and Mullah, K.B., inventors; AppliedBiosystems (Foster City, CA), assignee. 2 Mar. 1999. Hybridization assay usingself-quenching fluorescence probe. United States patent 5,876,930.Livak, K.J., Marmaro, J., and Todd, J.A. 1995. Towards fully automatedgenome-wide polymorphism screening [letter]. Nat. Genet. 9:341–342.Martens, H. and Naes, T., 1989. In: Multivariate Calibration, John Wiley & Sons,Chichester.de Kok, J.B., Hendriks, J.C., van Solinge, W.W., Willems, H.L., Mensink, E.J., andSwinkels, D.W. Use of real-time quantitative PCR to compare DNA isolationmethods. Clin.Chem. 44(10):2201-2204, 1998.Goldsworthy, S.M., Stockton, P.S., Trempus, C.S., Foley, J.F., and Maronpot, R.R.Effects of fixation on RNA extraction and amplification from laser capturemicrodissected tissue. Mol.Carcinog. 25(2):86-91, 1999.Kruse, N., Pette, M., Toyka, K., and Rieckmann, P. Quantification of cytokine mRNAexpression by RT PCR in samples of previously frozen blood. J.Immunol.Methods210(2):195-203, 1997.Lie, Y. S. and C. J., Petropoulos. "Advances in quantitative PCR technology:5' nuclease assays." Curr Opin Biotechnol 9 (1998): 43-48.Orlando, C., P. , Pinzani, and M. , Pazzagli. "Developments in quantitative PCR."Clin Chem Lab Med 36 (1998): 255-269.Smetsers, T.F., Stevens, E.H., van de Locht, L.T., and Mensink, E.J. Freezing of PCRmaster mixture retains full amplification activity and facilitates PCR standardisationfor molecular diagnostics and real-time quantitative PCR [letter]. Leukemia12(8):1324-1325, 1998.Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide Bibliography-1DRAFTSeptember 1, 2004 11:38 am, Bibliography.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
Page 307 and 308: TaqMan Low Density ArrayTable 8-6Tr
Page 309 and 310: Software ReferenceAAIn This Appendi
Page 311 and 312: Importing Plate Document Setup Tabl
Page 313 and 314: Setup Table Files1. File VersionDes
Page 315 and 316: Setup Table Files6. Detectors ListD
Page 317 and 318: Setup Table Files9. Markers List (A
Page 319 and 320: Setup Table FilesFormat(for a singl
Page 321 and 322: Setup Table FilesFormat(for a singl
Page 323 and 324: Setup Table FilesExample Code A-16A
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
Page 331 and 332: Connecting SDS Software to the Data
Page 333 and 334: Designing TaqMan Reagent-BasedAssay
Page 335 and 336: Assay Development Guidelines• For
Page 337 and 338: Design Tips for Allelic Discriminat
Page 339 and 340: Kits, Reagents, and ConsumablesCCIn
Page 341 and 342: Consumables and DisposablesConsumab
Page 343 and 344: Instrument Maintenance and Verifica
Page 345 and 346: Custom Oligonucleotide SynthesisTab
Page 347 and 348: Theory of OperationDDIn This Append
Page 349 and 350: Fluorescent-Based ChemistriesBasics
Page 351 and 352: Real-Time Data AnalysisPhase 2: Lin
Page 353 and 354: Real-Time Data AnalysisSignificance
Page 355 and 356: A similar equation for the endogeno
Page 357: Limited Warranty StatementEEWarrant
Page 361 and 362: Klein, D., Janda, P., Steinborn, R.
Page 363 and 364: Dolken, L., F. , Schuler, and G. ,
Page 365 and 366: AllelicDiscriminationVirtanen M., H
Page 367 and 368: Glossary.sdd.sdm.sds.sdt∆C T∆
Page 369 and 370: ackgroundbaselinecalibratorcDNA(com
Page 371 and 372: minor groovebinder (MGB)multicompon
Page 373 and 374: R nrunsessionsingle nucleotidepolym
Page 375 and 376: IndexSymbols- 6-31↑ 6-33Numerics7
Page 377 and 378: fluorescent, common sources 8-7isol
Page 379 and 380: adjusting step parameters 3-21confi
Page 381 and 382: sample block locking bar 7-8sample
Page 384: Worldwide Sales and SupportApplied
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