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

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Chapter 8TroubleshootingSDS Enterprise DatabaseSDS EnterpriseDatabaseTroubleshootingTableTable 8-7Troubleshooting the SDS Enterprise DatabaseObservation Possible Cause Recommended ActionCannot Connect to theDatabaseN/ATo test or reset the databaseconnection:1. Start the SDS software.2. Log into the database asa user withAdministrative privileges3. Test and reconfigure thedatabase connection asdescribed in“Reconfiguring theDatabase Connection”on page A-23.Error message:java.sql.SQLException:Io exception: End ofTNS data channelRare error whenarchiving or restoring alarge data setReattempt the archive orrestoration task.8-20 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_Trouble.fm
Software ReferenceAAIn This Appendix Importing Plate Document Setup Table Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2Setup Table Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4Exporting Graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-16Exporting Plate Document Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-16Operating the SDS Software from a Command Line . . . . . . . . . . . . . . . . . . . . . A-18Using the Search Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-20Connecting SDS Software to the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-22Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide A-1DRAFTSeptember 1, 2004 11:39 am, App_SWReference.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
Page 257 and 258: Performing a Pure Dye RunAnalyzing
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Page 263 and 264: Verifying Instrument PerformanceTab
Page 265 and 266: Verifying Instrument PerformancePre
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Page 269 and 270: Adjusting the Sensitivity of the Pl
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Page 275 and 276: Aligning the Plate Handler5. Using
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Page 283 and 284: Aligning the Fixed-Position Bar Cod
Page 285 and 286: Section 7.3 Maintaining the Compute
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Page 289 and 290: Troubleshooting 88In This Chapter T
Page 291 and 292: Troubleshooting TableTable 8-1Troub
Page 293 and 294: Low Precision or IrreproducibilityL
Page 295 and 296: Low Precision or IrreproducibilityD
Page 297 and 298: Background RunsBackground RunsBackg
Page 299 and 300: Pure Dye Runs6. Repeat step 4 until
Page 301 and 302: End-Point Runs (Allelic Discriminat
Page 303 and 304: Software and 7900HT InstrumentTable
Page 305 and 306: Zymark Twister Microplate Handler a
Page 307: TaqMan Low Density ArrayTable 8-6Tr
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 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
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Page 357 and 358: 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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