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

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Chapter 7Maintaining the InstrumentAutomation Accessory Components and Stack PositionsAutomationAccessoryComponentsRefer to Figure 7-5 for the components discussed in this section.(cross-sectional view of the gripper)GR2014aPlate-sensorswitchGripperAdjustmentknobPlate stackExpansion stacksZymark Twister Microplate HandlerFixed-position bar code readerFigure 7-5Components of the Automation AccessoryPlate StackPositionsThe Zymark Twister Microplate Handler alignment is performed using the Zymark ®Twister Software. The software refers to the positions of the plate stacks differentlythan the Automation Controller Software. Figure 7-6 lists the positions defined bythe Zymark Twister Software and the Automation Controller Software equivalents.107Zymark TwisterSoftwareAutomationControllerSoftware26Position 0Output345Position 1Position 2(unused)Instrument(front of instrument)Bar codeWell A1Position 3(unused)Position 4 Stack 1Figure 7-6Positions of the Automation Controller and Zymark Twister Software7-36 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_Maintenance.fm
Adjusting the Sensitivity of the Plate Sensor SwitchAdjusting the Sensitivity of the Plate Sensor SwitchWhen to PerformMaterialsRequiredAdjusting thePlate SensorSwitchThe plate sensor switch located underneath the arm of the Zymark TwisterMicroplate Handler requires adjustment under the following circumstances:• When changing sample block module formats• If the Plate Handler is having difficulty sensing plates• Optical plate (of the current sample block format)The dimensions of different plate formats can place different requirements on howthe Plate Handler grips plates. To ensure smooth operation of the AutomationAccessory, adjust the plate sensor switch when changing consumable formats.1. Power off the Zymark Twister Microplate Handler.PHYSICAL HAZARD. The Zymark Twister MicroplateHandler must be powered off at all times during the following procedure. Failureto comply can result in physical injury to the user or damage to the PlateHandler.2. Clear the switch position by turning the thumb wheel all the way to the Upextreme (as indicated on the side panel).Thumb wheelGR2014aPlate-sensor switch3. Begin the adjustment of the sensor switch:a. Grasp an optical plate by the sides, making sure not to place pressure in thecenter of the plate to deform it.b. Place the plate between the fingers of the gripper assembly and align it tothe middle of the centering device.c. While holding the plate in position, slowly turn the thumb wheel to lowerthe switch onto the reaction plate until the switch:– Contacts the top of the plate, and– Emits a soft, audible “clicking” noiseIMPORTANT! The sound emitted by the sensor switch is very faint and may bedifficult to hear. To make the adjustment easier, place your ear close to thesensor switch while making the adjustment and listen for the switch to engage.Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide 7-37DRAFTSeptember 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
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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
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 and 236: Notes for Database UsersDescription
Page 237 and 238: Section 7.1 Maintaining the 7900HT
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
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Page 263 and 264: Verifying Instrument PerformanceTab
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Page 289 and 290: Troubleshooting 88In This Chapter T
Page 291 and 292: Troubleshooting TableTable 8-1Troub
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Page 297 and 298: Background RunsBackground RunsBackg
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Page 301 and 302: End-Point Runs (Allelic Discriminat
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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
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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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