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

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© Copyright 2004, Applied Biosystems. All rights reserved.For Research Use Only. Not for use in diagnostic procedures.Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. Thisdocument is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, orconsequential damages in connection with or arising from the use of this document.AUTHORIZED THERMAL CYCLER: This Applied Biosystems 7900HT Fast Real-Time PCR System Base Unit, Serial No___________, in combination with itsimmediately attached sample block modules, comprise an Authorized Thermal Cycler. The purchase price of this Base Unit includes the up-front fee component of alicense under United States Patent Nos. 4,683,195, 4,683,202 and 4,965,188, owned by Roche Molecular Systems, Inc., and under corresponding claims in patentsoutside the United States, owned by F. Hoffmann-La Roche Ltd, covering the Polymerase Chain Reaction (“PCR”) process to practice the PCR process for internalresearch and development using this instrument. The running royalty component of that license may be purchased from Applied Biosystems or obtained by purchasingAuthorized Reagents. This instrument is also an Authorized Thermal Cycler for use with applications licenses available from Applied Biosystems. Its use withAuthorized Reagents also provides a limited PCR license in accordance with the label rights accompanying such reagents. Purchase of this product does not itselfconvey to the purchaser a complete license or right to perform the PCR process. Further information on purchasing licenses to practice the PCR process may beobtained by contacting the Director of Licensing at Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404.DISCLAIMER OF LICENSE: No rights for any application, including any in vitro diagnostic application, are conveyed expressly, by implication or by estoppelunder any patent or patent applications claiming homogeneous or real-time detection methods, including patents covering such methods used in conjunction with thePCR process or other amplification processes. The 5' nuclease detection assay and certain other homogeneous or real-time amplification and detection methods arecovered by United States Patent Nos. 5,210,015, 5,487,972, 5,804,375 and 5,994,056, owned by Roche Molecular Systems, Inc.; by corresponding patents and patentapplications outside the United States, owned by F. Hoffmann-La Roche Ltd; and by United States Patent Nos. 5,538,848 and 6,030,787, and corresponding patentsand patent applications outside the United States, owned by Applera Corporation. Purchase of this instrument conveys no license or right under the foregoing patents.Use of these and other patented processes in conjunction with the PCR process requires a license. For information on obtaining licenses, contact the Director ofLicensing at Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, or The Licensing Department, Roche Molecular Systems, Inc., 1145Atlantic Avenue, Alameda, California, 94501NOTICE TO PURCHASER: PLEASE REFER TO THE SDS ENTERPRISE DATABASE USER'S MANUAL FOR LIMITED LABEL LICENSE ORDISCLAIMER INFORMATION.JpegEncoder Licensing StatementThe JpegEncoder and its associated classes are Copyright © 1998, James R. Weeks and BioElectroMech. This software is based in part on the work of the IndependentJPEG Group.Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:1. Redistributions of source code must retain the above copyright notice, this list of conditions, all files included with the source code, and the following disclaimer.2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or othermaterials provided with the distribution.THIS SOFTWARE (JpegEncoder) IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES,INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AREDISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER INCONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THISSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.TRADEMARKS:ABI PRISM, Applied Biosystems, MicroAmp, Primer Express, and VIC are registered trademarks and AB (Design), ABI PRISM, Applera, FAM, JOE, NED, ROX,TAMRA, and TET are trademarks of Applera Corporation or its subsidiaries in the US and/or certain other countries.AmpErase, AmpliTaq Gold, GeneAmp, and TaqMan are registered trademarks of Roche Molecular Systems, Inc.SYBR is a registered trademark of Molecular Probes, Inc.Zymark is a registered trademark of Zymark Corporation.Windows and Windows NT are registered trademarks of Microsoft Corporation.All other trademarks are the sole property of their respective owners.Part Number 4351684 Rev. A09/2004DRAFTSeptember 1, 2004 11:38 am, 4351684A_Title.fm
ContentsPrefaceHow to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiHow to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiiHow to Obtain Services and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiiSafety and EMC Compliance InformationSafety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xivSymbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvSafety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviGeneral Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviiChemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviiiChemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xixElectrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxPhysical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiBiological Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiLaser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiBar Code Scanner Laser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiiWorkstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxiiiSafety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . . . . . xxiiiChapter 1Product OverviewSystem Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2Section 1.1 Getting to Know the Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-37900HT Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6Bar Code Readers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7Zymark Twister Microplate Handler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8Compatible Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-9Instrument Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10Section 1.2 Getting to Know the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-13Software Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-14SDS Software Related Files and Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:40 am, 4351684ATOC.fmiii
Page 1: Applied Biosystems7900HT Fast Real-
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 and 46: Section 1.3 SDS Enterprise Database
Page 47 and 48: * + Enter* +Enter3Down UpNumLockSys
Page 49 and 50: About the SDS Enterprise Database S
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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
Page 89 and 90:
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
Page 197 and 198:
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
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Performing a Pure Dye RunAnalyzing
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Adding Custom Dyes to the Pure Dye
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Adding Custom Dyes to the Pure Dye
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Verifying Instrument PerformanceTab
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Verifying Instrument PerformancePre
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Section 7.2 Maintaining the Plate H
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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
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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
Page 327 and 328:
Operating the SDS Software from a C
Page 329 and 330:
Using the Search ToolLogical Operat
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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
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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.
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
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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
Page 381 and 382:
sample block locking bar 7-8sample
Page 384:
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