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

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Appendix CKits, Reagents, and ConsumablesTable C-2Consumables and Disposables for the 7900HT InstrumentPart No. Description Quantity96-Well Optical Reaction Plates4306737 ABI PRISM 96-Well Optical Reaction Plate with Barcode(code 128)4326659 ABI PRISM 96-Well Optical Reaction Plate with Barcode(code 128), 25-PackIncludes 25 of PN 4306737, ABI PRISM 96-Well OpticalReaction Plates with Barcode4314320 ABI PRISM 96-Well Optical Reaction Plate with Barcode(code 128) and ABI PRISM Optical Adhesive CoversIncludes 100 ABI PRISM Optical Adhesive Covers(PN 4311971) and 5 of PN 4306737, ABI PRISM 96-WellOptical Reaction Plates with Barcode4312063 MicroAmp ® Splash Free Support Base for 96-Well ReactionPlates20 Plates500 Plates100 Plates100 Covers10 BasesOptical 96-Well Fast Plates4346906 Optical 96-Well Fast Thermal Cycling Plate with Barcode(code 128)4312063 MicroAmp ® Splash Free Support Base for 96-Well ReactionPlates20 Plates10 BasesC-4 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, App_Consumables.fm
Instrument Maintenance and VerificationInstrument Maintenance and VerificationThe following sequence detection kits and reagents are used to perform routinemaintenance on and verify the function of the Applied Biosystems 7900HT FastReal-Time PCR System. For more information about the use of the kits below, seeChapter 7, “Maintaining the Instrument.”Table C-3Consumables for Instrument Maintenance and VerificationPartNumberDescriptionQuantitySequence Detection Systems Spectral Calibration Kits4328639 ABI PRISM 7900HT Sequence Detection Systems 96-WellSpectral Calibration KitIncludes three ABI PRISM 96-Well Optical Reaction Plates:one preloaded and sealed background plate, and twopreloaded and sealed Spectral Calibration plates containingeight separate dye standards (FAM , JOE , NED , ROX ,SYBR ® Green, TAMRA , TET , VIC ® ).4323977 Sequence Detection Systems 384-Well Spectral CalibrationKitIncludes two ABI PRISM 384-Well Optical Reaction Plates:one preloaded and sealed background plate and onepreloaded and sealed Spectral Calibration plate containingeight separate dye standards (FAM, JOE, NED, ROX, SYBRGreen, TAMRA, TET, VIC).4351653 7900HT System Fast 96-Well Spectral Calibration KitIncludes three Optical 96-Well Fast Thermal Cycling Plates:one preloaded and sealed background plate, and twopreloaded and sealed pure dye plates containing eightseparate dye standards (FAM , JOE , NED , ROX , SYBR ®Green, TAMRA , TET , VIC ® ).3 x 96-WellPlates2x384-WellPlates3 x 96-WellPlatesTaqMan RNase P Instrument Verification Plates4310982 TaqMan ® RNase P Instrument Verification PlateIncludes one ABI PRISM 96-Well Optical Reaction Plate. Eachwell contains preloaded reaction mix (master mix, RNase Pprimers, and FAM dye-labeled probe) and template to detectand quantitate genomic copies of the human RNase P gene.4323306 TaqMan ® RNase P 384-Well Instrument Verification PlateIncludes one ABI PRISM 384-Well Optical Reaction Plate.Each well contains preloaded reaction mix (master mix,RNase P primers, and FAM dye-labeled probe) and templateto detect and quantitate genomic copies of the humanRNase P gene.1 x 96-WellPlate1 x384-WellPlateApplied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide C-5DRAFTSeptember 1, 2004 11:39 am, App_Consumables.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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Page 297 and 298: Background RunsBackground RunsBackg
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Page 303 and 304: Software and 7900HT InstrumentTable
Page 305 and 306: 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
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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: Consumables and DisposablesConsumab
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 and 358: Limited Warranty StatementEEWarrant
Page 359 and 360: BibliographyGeneral Paperson TaqMan
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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