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

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Chapter 6Analyzing Real-Time Data• If analyzing a Relative Quantification Multiple Plate Document, view theresults of the run displayed within the Gene Expression plot andResults table.Eliminating Wellsfrom the AnalysisThe SDS software allows you to omit wells from the analysis. If you have identifiedoutliers or data you want to exclude from the analysis, follow the procedure below toremove the corresponding wells from use.IMPORTANT! If a well is removed from use before the plate document is run, theSDS software does not collect data for the well during the run. However, if a well isremoved from use after the plate document has been run, the software excludes thewell from the analysis but does not delete the data.1. If omitting wells from a Relative Quantification Multiple Plate Document,select a plate in the Plates field that contains wells you want to omit.2. While pressing and holding the Ctrl key, select the well(s) in the plate grid thatyou want to omit.3. If omitting wells from a Relative Quantification Multiple Plate Document,repeat steps 1 through 2 for each plate in the study.4. Select the Setup tab.5. In the well inspector, click the Omit Well(s) check box to exclude the selectedwells from the analysis.Selected wells(removed from use)Omit Well(s) check box(selected)Note: To reinstate an omitted well, select the well, then click the Omit Well(s)check box.6-50 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_Real-Time.fm
Eliminating Outlying Amplification6. Click (or select Analysis > Analyze).7. Repeat the procedures in “Visualizing Outliers” on page 6-49 to verify that alloutliers have been removed from the analysis.Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide 6-51DRAFTSeptember 1, 2004 11:39 am, CH_Real-Time.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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Notes for Database UsersDescription
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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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Page 177 and 178: After the AnalysisSaving theResults
Page 179 and 180: Analyzing Real-Time Data 66In This
Page 181 and 182: Notes for Database UsersDescription
Page 183 and 184: 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
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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
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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
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
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Page 275 and 276: Aligning the Plate Handler5. 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
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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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