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

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Chapter 7Maintaining the InstrumentRecommended Maintenance ScheduleMaintenanceScheduleThe following table includes a list of tasks that should be performed on theApplied Biosystems 7900HT Fast Real-Time PCR System regularly.Table 7-1Maintenance Schedule for the 7900HT InstrumentInterval Task See PageSu M T W Th F SArchive SDS Files 7-54Week (7 Days)Su M T W Th F SPerform a Background Run 7-16Check (and if necessary replace) Gripper FingerPads7-52Month (30 Days)Defragment the Computer Hard Drive 7-54JanuaryJulyPerform a Pure Dye Run *7-20Su M T W Th F SSu M T W Th F SSemi-Annually(6 Months)Check Applied Biosystems Web Site for SoftwareUpdates7-55*Perform a background run before each Pure Dye Run.7-4 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_Maintenance.fm
Section 7.1 Maintaining the 7900HT InstrumentSection 7.1Maintaining the 7900HT InstrumentIn This Section Replacing the Sample Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6Changing the Plate Adapter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12Decontaminating the Sample Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14Performing a Background Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16Performing a Pure Dye Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20Adding Custom Dyes to the Pure Dye Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27Verifying Instrument Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide 7-5DRAFTSeptember 1, 2004 11:39 am, CH_Maintenance.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
Page 185 and 186: OverviewAlgorithmicManipulation ofR
Page 187 and 188: Analysis ChecklistAnalysis Checklis
Page 189 and 190: Analyzing the DataAnalyzing the Dat
Page 191 and 192: Viewing ResultsViewing ResultsViewi
Page 193 and 194: Section 6.2 Relative Quantification
Page 195 and 196: OverviewAlgorithmic Manipulation of
Page 197 and 198: OverviewAutomatic Outlier RemovalAb
Page 199 and 200: Getting StartedGetting StartedUsing
Page 201 and 202: Options for Analyzing Relative Quan
Page 203 and 204: Creating the Studyd. In the Plate Q
Page 205 and 206: Analyzing the Study• Manual Ct -
Page 207 and 208: Analyzing the StudySpecifying the A
Page 209 and 210: Viewing ResultsViewing ResultsDispl
Page 211 and 212: Viewing ResultsAbout DownArrowsDown
Page 213 and 214: After the AnalysisAfter the Analysi
Page 215 and 216: Section 6.3 Dissociation Curve Anal
Page 217 and 218: Before You BeginExample ResultsFigu
Page 219 and 220: Opening the Run DataOpening the Run
Page 221 and 222: Determining T m Values for the Anal
Page 223 and 224: Section 6.4 Procedure ReferenceSect
Page 225 and 226: Setting the Baseline and Threshold
Page 227 and 228: Eliminating Outlying AmplificationE
Page 229 and 230: Eliminating Outlying Amplification6
Page 231 and 232: After the AnalysisSaving theResults
Page 233 and 234: Maintaining the Instrument 77In Thi
Page 235: Notes for Database UsersDescription
Page 239 and 240: Replacing the Sample BlockMaterials
Page 241 and 242: Replacing the Sample Block9. Loosen
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Page 245 and 246: Changing the Plate Adapter4. Place
Page 247 and 248: Decontaminating the Sample BlockCle
Page 249 and 250: Performing a Background RunPreparin
Page 251 and 252: Performing a Background RunAnalyzin
Page 253 and 254: Performing a Pure Dye RunAfter a ru
Page 255 and 256: Performing a Pure Dye Run• Fast 9
Page 257 and 258: Performing a Pure Dye RunAnalyzing
Page 259 and 260: Adding Custom Dyes to the Pure Dye
Page 261 and 262: Adding Custom Dyes to the Pure Dye
Page 263 and 264: Verifying Instrument PerformanceTab
Page 265 and 266: Verifying Instrument PerformancePre
Page 267 and 268: Section 7.2 Maintaining the Plate H
Page 269 and 270: Adjusting the Sensitivity of the Pl
Page 271 and 272: Adjusting the Sensitivity of the Pl
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Page 275 and 276: Aligning the Plate Handler5. Using
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Page 279 and 280: Aligning the Plate Handler13. Click
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Page 283 and 284: Aligning the Fixed-Position Bar Cod
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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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