General Paperson AbsoluteQuantitationArnold, B.A., Hepler, R.W., <strong>and</strong> Keller, P.M. One-Step Fluorescent ProbeProduct-Enhanced Reverse Transcriptase Assay. BioTechniques 25(1):98-106, 1998.Ambs S., S. Dennis, J. Fairman, M. Wright <strong>and</strong> J. Papkoff. 1999. Inhibition of tumorgrowth correlates with the expression level of a human angiostatin transgene intransfected B16F10 melanoma cells [In Process Citation]. Cancer Res. 59:5773-5777,1999.Becker K., D. Pan <strong>and</strong> C.B. Whitley. 1999. <strong>Real</strong>-time quantitative polymerase chainreaction to assess gene transfer. Hum. Gene Ther. 10:2559-2566, 1999.Berg, T., M ller, A.R., Platz, K.P., Hohne, M., Bechstein, W.O., Hopf, U.,Wiedenmann, B., Neuhaus, P., <strong>and</strong> Schreier, E. Dynamics of GB virus C viremia earlyafter orthotopic liver transplantation indicates extrahepatic tissues as the predominantsite of GB virus C replication. Hepatology 29(1):245-249, 1999.Chiang, P.W., Wei, W.L., Gibson, K., Bodmer, R., <strong>and</strong> Kurnit, D.M. A fluorescentquantitative <strong>PCR</strong> approach to map gene deletions in the Drosophila genome [InProcess Citation]. Genetics 153(3):1313-1316, 1999.de Kok, J.B., Hendriks, J.C., van Solinge, W.W., Willems, H.L., Mensink, E.J., <strong>and</strong>Swinkels, D.W. Use of real-time quantitative <strong>PCR</strong> to compare DNA isolation methods.Clin.Chem. 44(10):2201-2204, 1998.Fairman, J., Roche, L., Pieslak, I., Lay, M., Corson, S., Fox, E., Luong, C., Koe, G.,Lemos, B., Grove, R., Fradkin, L., <strong>and</strong> Vernachio, J. Quantitative RT-<strong>PCR</strong> to evaluatein vivo expression of multiple transgenes using a common intron [In Process Citation].BioTechniques 27(3):566-70, 572-4, 1999.Gerard, C. J., et al. "Improved quantitation of minimal residual disease in multiplemyeloma using real-time polymerase chain reaction <strong>and</strong> plasmid-DNAcomplementarity determining region III st<strong>and</strong>ards." Cancer Res 58 (1998):3957-3964.Hartel, C., Bein, G., Kirchner, H., <strong>and</strong> Kluter, H. A Human Whole-Blood Assay forAnalysis of T-Cell Function by Quantification of Cytokine mRNA. Sc<strong>and</strong>.J.Immunol.49(6):649-654, 1999.Higgins, J. A., et al. "5' nuclease <strong>PCR</strong> assay to detect Yersinia pestis [In ProcessCitation]." J Clin Microbiol 36 (1998): 2284-2288.Hennig, H., et al. "Lack of evidence for Marek's disease virus genomic sequences inleukocyte DNA from multiple sclerosis patients in Germany [In Process Citation]."Neurosci Lett 250 (1998): 138-140.Houng, H.H., Hritz, D., <strong>and</strong> Kanesa-thasan, N. Quantitative detection of dengue 2virus using fluorogenic RT-<strong>PCR</strong> based on 3'-noncoding sequence. J.Virol.Methods2000.Apr;86(1):1-11.Kafert S., J. Krauter, A. Ganser <strong>and</strong> M. Eder. Differential quantitation of alternativelyspliced messenger RNAs using isoform-specific real-time RT-<strong>PCR</strong>. Anal. Biochem.269:210-213, 1999.Kimura, H., Morita, M., Yabuta, Y., Kuzushima, K., Kato, K., Kojima, S., Matsuyama,T., <strong>and</strong> Morishima, T. Quantitative analysis of Epstein-Barr virus load by using areal-time <strong>PCR</strong> assay. J.Clin.Microbiol. 37(1):132-136, 1999.
Klein, D., J<strong>and</strong>a, P., Steinborn, R., Muller, M., Salmons, B., <strong>and</strong> Gunzburg, W.H.Proviral load determination of different feline immunodeficiency virus isolates usingreal-time polymerase chain reaction: influence of mismatches on quantification [InProcess Citation]. Electrophoresis 20(2):291-299, 1999.Lo, Y. M., et al. "Quantitative analysis of fetal DNA in maternal plasma <strong>and</strong> serum:implications for noninvasive prenatal diagnosis." Am J Hum Genet 62 (1998):768-775.Lo, Y.M., Chan, L.Y., Lo, K.W., Leung, S.F., Zhang, J., Chan, A.T., Lee, J.C., Hjelm,N.M., Johnson, P.J., <strong>and</strong> Huang, D.P. Quantitative analysis of cell-free Epstein-Barrvirus DNA in plasma of patients with nasopharyngeal carcinoma. Cancer Res.59(6):1188-1191, 1999.Lo, Y.M., Leung, T.N., Tein, M.S., Sargent, I.L., Zhang, J., Lau, T.K., Haines, C.J., <strong>and</strong>Redman, C.W. Quantitative abnormalities of fetal DNA in maternal serum inpreeclampsia [see comments]. Clin.Chem. 45(2):184-188, 1999.Lo Y.M., L.Y. Chan, A.T. Chan, S.F. Leung, K.W. Lo, J. Zhang, J.C. Lee, N.M. Hjelm,P.J. Johnson <strong>and</strong> D.P. Huang. 1999. Quantitative <strong>and</strong> temporal correlation betweencirculating cell-free Epstein-Barr virus DNA <strong>and</strong> tumor recurrence in nasopharyngealcarcinoma. Cancer Res. 59:5452-5455.Leutenegger, C.M., Klein, D., Hofmann-Lehmann, R., Mislin, C., Hummel, U., Boni,J., Boretti, F., Guenzburg, W.H., <strong>and</strong> Lutz, H. Rapid feline immunodeficiency virusprovirus quantitation by polymerase chain reaction using the TaqMan fluorogenicreal-time detection system [In Process Citation]. J.Virol.Methods 78(1-2):105-116,1999Lockey, C., E. , Otto, <strong>and</strong> Z. , Long. "<strong>Real</strong>-time fluorescence detection of a singleDNA molecule." BioTechniques 24 (1998): 744-746.Luthra, R., et al. "Novel 5' exonuclease-based real-time <strong>PCR</strong> assay for the detection oft(14;18)(q32;q21) in patients with follicular lymphoma." Am J Pathol 153 (1998):63-68.Maudru, T. <strong>and</strong> K. W., Peden. "Adaptation of the fluorogenic 5'-nuclease chemistry toa <strong>PCR</strong>-based reverse transcriptase assay." BioTechniques 25 (1998): 972-975.Nagai, M., Usuku, K., Matsumoto, W., Kodama, D., Takenouchi, N., Moritoyo, T.,Hashiguchi, S., Ichinose, M., Bangham, C.R., Izumo, S., <strong>and</strong> Osame, M. Analysis ofHTLV-I proviral load in 202 HAM/TSP patients <strong>and</strong> 243 asymptomatic HTLV-Icarriers: high proviral load strongly predisposes to HAM/TSP. J.Neurovirol.4(6):586-593, 1998.Nogva, H.K. <strong>and</strong> Lillehaug, D. Detection <strong>and</strong> quantification of Salmonella in purecultures using 5'-nuclease polymerase chain reaction [In Process Citation]. Int.J.FoodMicrobiol. 51(2-3):191-196, 1999.Pusterla, N., Huder, J.B., Leutenegger, C.M., Braun, U., Madigan, J.E., <strong>and</strong> Lutz, H.Quantitative real-time <strong>PCR</strong> for detection of members of the Ehrlichia phagocytophilagenogroup in host animals <strong>and</strong> Ixodes ricinus ticks. J.Clin.Microbiol.37(5):1329-1331, 1999.Pusterla, N., Leutenegger, C.M., Chae, J.S., Lutz, H., Kimsey, R.B., Dumler, J.S., <strong>and</strong>Madigan, J.E. Quantitative Evaluation of Ehrlichial Burden in Horses afterExperimental Transmission of Human Granulocytic Ehrlichia Agent by IntravenousInoculation with Infected Leukocytes <strong>and</strong> by Infected Ticks. J.Clin.Microbiol.37(12):4042-4044, 1999.<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 Guide Bibliography-3DRAFTSeptember 1, 2004 11:38 am, Bibliography.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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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 2 - Applying Detectors and Mar
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Step 2 - Applying Detectors and Mar
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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 5 - Programming 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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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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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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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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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 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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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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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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- Page 359: BibliographyGeneral Paperson TaqMan
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