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

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Chapter 1Product OverviewAbout the SDS Enterprise Database FeatureAbout theDatabaseAccess ControlNetworkArchitectureThe SDS software can interface directly with an Applied Biosystems SDS EnterpriseDatabase as part of a laboratory information management system (LIMS). The SDSEnterprise Database is a relational, Oracle-based repository designed specifically tostore SDS data produced by an Applied Biosystems 7900HT Fast Real-Time PCRSystem. In addition to serving as a common repository for SDS data, the databaseprovides user authentication, robust and scalable data management, and flexiblearchive capabilities. The database also provides the infrastructure and tools necessaryto integrate a 7900HT instrument into a laboratory workflow made up of existingdata management solutions.The SDS Enterprise Database provides a multi-level user security system thatrestricts access to the database and to most functions of the SDS software and7900HT instrument. The database provides the SDS User Account Manager softwarewith the client version of the SDS software for managing user accounts. The UserManager allows users with Administrator privileges to assign privileges andpasswords for user accounts, and to add and remove them. This guide indicates theaccess privileges required to perform each task using a short note above eachprocedure.Note: See the SDS Enterprise Database for the Applied Biosystems 7900HT FastReal-Time PCR System Administrators Guide (PN 4351669) for a completedescription of user accounts for the SDS Enterprise Database.The SDS Enterprise Database is a relational, Oracle-based repository designed to storeSDS data produced by Applied Biosystems 7900HT Fast Real-Time PCR Systeminstruments. In addition to serving as a common repository for SDS data, the databaseprovides user authentication, robust and scalable data management, and flexible archivecapabilities. The database also provides the infrastructure and tools necessary tointegrate a 7900HT instrument into a laboratory workflow made up of existing datamanagement solutions.The SDS Enterprise Database supports a basic two-tier, server-client architecturewithin an Ethernet (10Base-T) or Fast Ethernet (100Base-T) network environment.The database can function as part of an isolated star network via the SMC routerprovided with the database (Figure 1-14), or as a node on a larger bus network(Figure 1-15). The server computer uses a static IP address to simultaneously serveup to 5 clients configured for either DHCP or static TCP/IP operation.1-22 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:38 am, CH_Overview.fm
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Page 1 and 2: Applied Biosystems7900HT Fast Real-
Page 3 and 4: ContentsPrefaceHow to Use This Guid
Page 5 and 6: Chapter 4Operating the InstrumentNo
Page 7 and 8: Chapter 7Maintaining the Instrument
Page 9 and 10: Appendix D Theory of OperationFluor
Page 11 and 12: PrefaceHow to Use This GuidePurpose
Page 13 and 14: Safety and EMC Compliance Informati
Page 15 and 16: Symbols on InstrumentsSymbols on In
Page 17 and 18: General Instrument SafetyGeneral In
Page 19 and 20: Chemical Waste SafetyChemical Safet
Page 21 and 22: Physical Hazard SafetyOvervoltageRa
Page 23 and 24: Workstation SafetyWorkstation Safet
Page 25 and 26: Product Overview 11In This Chapter
Page 27 and 28: 7900HT FAST Real-Time PCR SystemSec
Page 29 and 30: 7900HT InstrumentInterchangeableThe
Page 31 and 32: 7900HT FAST Real-Time PCR SystemBar
Page 33 and 34: Compatible ConsumablesCompatible Co
Page 35 and 36: Instrument ConnectionsFixed-Positio
Page 37 and 38: Section 1.2 Getting to Know the Sof
Page 39 and 40: SDS Software Related Files and Form
Page 41 and 42: 7900HT FAST Real-Time PCR SystemMan
Page 43 and 44: Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
Page 45: Section 1.3 SDS Enterprise Database
Page 49 and 50: About the SDS Enterprise Database S
Page 51 and 52: Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
Page 53 and 54: Getting Started 22In This Chapter G
Page 55 and 56: Getting StartedUsing the SDSSoftwar
Page 57 and 58: GR23967900HTPowering On the 7900HT
Page 59 and 60: Using the SDS SoftwareUsing the SDS
Page 61 and 62: Using the SDS SoftwareAbout theMess
Page 63 and 64: Basic Software Skills TutorialNotes
Page 65 and 66: Basic Software Skills TutorialExerc
Page 67 and 68: Basic Software Skills TutorialExpor
Page 73 and 74: Basic Software Skills TutorialLesso
Page 77 and 78: Basic Software Skills Tutorial3. Se
Page 81 and 82: Using SDS Plate DocumentsUsing SDS
Page 83 and 84: Using SDS Plate DocumentsWell Inspe
Page 85 and 86: Preparing a Run 33In This Chapter N
Page 87 and 88: Notes for Database UsersDescription
Page 89 and 90: Workflow OverviewWorkflow OverviewE
Page 91 and 92: Workflow OverviewAllelicDiscriminat
Page 93 and 94: Step 1 - Creating a Plate DocumentS
Page 95 and 96: Step 2 - Applying Detectors and Mar
Page 97 and 98:
Step 2 - Applying Detectors and Mar
Page 99 and 100:
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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Page 107 and 108:
Page 109 and 110:
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
Page 117 and 118:
Notes for Database UsersDescription
Page 119 and 120:
Section 4.1 Consumable PreparationS
Page 121 and 122:
Compatible ConsumablesTable 4-1Comp
Page 123 and 124:
Preparing Optical Plates for Usea.
Page 125 and 126:
Preparing TaqMan Low Density Arrays
Page 127 and 128:
Page 129 and 130:
Page 131 and 132:
Page 133 and 134:
Page 135 and 136:
Page 137 and 138:
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
Page 149 and 150:
Operating the Software without an S
Page 151 and 152:
Page 153 and 154:
Page 155 and 156:
Running Plates Using the Automation
Page 157 and 158:
Running Plates Using the Automation
Page 159 and 160:
Analyzing End-Point Data 55In This
Page 161 and 162:
Notes for Database UsersNotes for D
Page 163 and 164:
Section 5.1 Allelic DiscriminationS
Page 165 and 166:
OverviewTable 5-1Signal and Sequenc
Page 167 and 168:
Before You BeginBefore You BeginUsi
Page 169 and 170:
Opening the Run DataOpening the Run
Page 171 and 172:
Calling and Scrutinizing Allelic Di
Page 173 and 174:
Page 175 and 176:
Page 177 and 178:
After the AnalysisSaving theResults
Page 179 and 180:
Analyzing Real-Time Data 66In This
Page 181 and 182:
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
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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
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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
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Setting the Baseline and Threshold
Page 227 and 228:
Eliminating Outlying AmplificationE
Page 229 and 230:
Eliminating Outlying Amplification6
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After the AnalysisSaving theResults
Page 233 and 234:
Maintaining the Instrument 77In Thi
Page 235 and 236:
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
Page 243 and 244:
7900HT FAST Real-Time PCR SystemRep
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
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Performing a Background RunAnalyzin
Page 253 and 254:
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
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
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Section 7.2 Maintaining the Plate H
Page 269 and 270:
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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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
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 and 308:
TaqMan Low Density ArrayTable 8-6Tr
Page 309 and 310:
Software ReferenceAAIn This Appendi
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Importing Plate Document Setup Tabl
Page 313 and 314:
Setup Table Files1. File VersionDes
Page 315 and 316:
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
Page 321 and 322:
Setup Table FilesFormat(for a singl
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
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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
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Klein, D., Janda, P., Steinborn, R.
Page 363 and 364:
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
Page 371 and 372:
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
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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