M<strong>and</strong>igers, C.M., Meijerink, J.P., Raemaekers, J.M., Schattenberg, A.V., <strong>and</strong> Mensink,E.J. Graft-versus-lymphoma effect of donor leucocyte infusion shown by real- timequantitative <strong>PCR</strong> analysis of t(14;18) [letter]. Lancet 352(9139):1522-1523, 1998.Marcucci, G., et al. "Detection of minimal residual disease in patients withAML1/ETO-associated acute myeloid leukemia using a novel quantitative reversetranscription polymerase chain reaction assay." Leukemia 12 (1998): 1482-1489.Mensink, E., et al. "Quantitation of minimal residual disease in Philadelphiachromosome positive chronic myeloid leukaemia patients using real-time quantitativeRT-<strong>PCR</strong>." Br J Haematol 102 (1998): 768-774.Moody, A., Sellers, S., <strong>and</strong> Bumstead, N. Measuring infectious bursal disease virusRNA in blood by multiplex real-time quantitative RT-<strong>PCR</strong>. Virol.Methods2000.Mar;85(1-2):55-64.Patterson, B. K., et al. "Repertoire of chemokine receptor expression in the femalegenital tract: implications for human immunodeficiency virus transmission." Am JPathol 153 (1998): 481-490.Pongers-Willemse, M.J., Verhagen, O.J., Tibbe, G.J., Wijkhuijs, A.J., de Haas, V.,Roovers, E., van der Schoot, C.E., <strong>and</strong> van Dongen, J.J. <strong>Real</strong>-time quantitative <strong>PCR</strong>for the detection of minimal residual disease in acute lymphoblastic leukemia usingjunctional region specific TaqMan probes. Leukemia 12(12):2006-2014, 1998.Pugazhenthi, S., Nesterova, A., Sable, C., Heidenreich, K.A., Boxer, L.M., Heasley,L.E., <strong>and</strong> Reusch, J.E. Akt/protein kinase B up-regulates Bcl-2 expression throughcAMP-response element-binding protein. J.Biol.Chem.2000.Apr.14;275(15):10761-6.Raggi, C.C., Bagnoni, M.L., Tonini, G.P., Maggi, M., Vona, G., Pinzani, P., Mazzocco,K., De Bernardi, B., Pazzagli, M., <strong>and</strong> Orl<strong>and</strong>o, C. <strong>Real</strong>-time quantitative <strong>PCR</strong> for themeasurement of MYCN amplification in human neuroblastoma with the TaqM<strong>and</strong>etection system. Clin.Chem. 45(11):1918-1924, 1999.Ringel, M.D., Balducci-Silano, P.L., Anderson, J.S., Spencer, C.A., Silverman, J.,Sparling, Y.H., Francis, G.L., Burman, K.D., Wartofsky, L., Ladenson, P.W., Levine,M.A., <strong>and</strong> Tuttle, R.M. Quantitative reverse transcription-polymerase chain reaction ofcirculating thyroglobulin messenger ribonucleic acid for monitoring patients withthyroid carcinoma. J.Clin.Endocrinol.Metab. 84(11):4037-4042, 1999.Sangoram, A. M., et al. "Mammalian circadian autoregulatory loop: a timelessortholog <strong>and</strong> mPer1 interact <strong>and</strong> negatively regulate CLOCK-BMAL1-inducedtranscription." Neuron 21 (1998): 1101-1113.Sgroi D.C., S. Teng, G. Robinson, R. LeVangie, J.R. Hudson, Jr. <strong>and</strong> A.G. Elkahloun.1999. In vivo gene expression profile analysis of human breast cancer progression.Cancer Res. 59:5656-5661.Shayesteh, L., Lu, Y., Kuo, W.L., Baldocchi, R., Godfrey, T., Collins, C., Pinkel, D.,Powell, B., Mills, G.B., <strong>and</strong> Gray, J.W. PIK3CA is implicated as an oncogene inovarian cancer [see comments]. Nat.Genet. 21(1):99-102, 1999.Shimokawa, T., et al. "Transcriptional regulation of muscle-specific genes duringmyoblast differentiation." Biochem Biophys Res Commun 246 (1998): 287-292.Taoufik, Y., Froger, D., Benoliel, S., Wallon, C., Dussaix, E., Delfraissy, J.F., <strong>and</strong>Lantz, O. Quantitative ELISA-polymerase chain reaction at saturation usinghomologous internal DNA st<strong>and</strong>ards <strong>and</strong> chemiluminescence revelation.Eur.Cytokine.Netw. 9(2):197-204, 1998.Bibliography-6 <strong>Applied</strong> <strong>Biosystems</strong> <strong>7900HT</strong> <strong>Fast</strong> <strong>Real</strong>-<strong>Time</strong> <strong>PCR</strong> <strong>System</strong> <strong>and</strong> <strong>SDS</strong> Enterprise Database User GuideDRAFTSeptember 1, 2004 11:38 am, Bibliography.fm
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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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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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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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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 TutorialExerc
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Basic Software Skills TutorialExerc
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Basic Software Skills TutorialLesso
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Basic Software Skills TutorialLesso
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Basic Software Skills Tutorial3. Se
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Basic Software Skills TutorialLesso
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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 6 - Saving the Plate Document
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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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Preparing TaqMan Low Density Arrays
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Preparing TaqMan Low Density Arrays
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Preparing TaqMan Low Density Arrays
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Preparing TaqMan Low Density Arrays
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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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Operating the Software with an SDS
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Operating the Software without an S
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Operating the Software without an S
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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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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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Notes for Database UsersDescription
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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 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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Notes for Database UsersDescription
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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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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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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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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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