ABI Prism® 7900HT Sequence Detection System ... - OpenWetWare

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Index Symbols >symbol 3-4 Numerics 7900HT instrument, See instrument 9600 emulation mode 4-14 A ABI Prism 7700 Sequence Detection System, emulating 4-14 ABI PRISM SDS Single Plate (*.sds) files See plate documents ABI PRISM SDS Template Document (*.sdt) files See templates absolute quantification about 6-4 to 6-5 analyzing data 6-7 to 6-14 assay development guidelines C-6 procedure checklist 6-7 selecting and preparing standards C-6 setting up (procedure checklist) 4-3 troubleshooting 8-11 adding bar code to a plate document 3-19, 4-19 custom dyes to the pure dye set 7-21 detector tasks to a plate document 4-11 detectors to a plate document 4-8 markers to a plate document 4-10 plate documents to the plate queue 4-31, 4-35 sample names to a plate document 4-19 adjusting analysis options for absolute quantification 6-8 display settings 4-17 method step parameters 4-15 plate-sensor switch 7-28 to 7-31 adjustment knob 7-27 air bubbles 8-5 aligning fixed-position bar code reader 7-40 to 7-42 plate handler 7-32 to 7-39 allele calls about 5-12 calling 5-11 scrutinizing 5-13 DRAFT December 11, 2001 8:32 pm 4317596IX.fm allelic discrimination about 5-4 to 5-6 analyzing run data 5-8 to 5-15 assay development guidelines C-5 maximizing throughput 4-2 procedure checklist 5-8 setting up (procedure checklist) 4-4 thermal cycling on the 7900HT instrument 4-14 troubleshooting 8-13 Allelic Discrimination Plot about 5-10 calling alleles 5-11 datapoint cluster variations 5-5 exporting as a graphic file B-8 exporting data as a text file B-9 genotypic segregation 5-6 outliers 5-6 scrutinizing allele calls 5-13 amplification curve about A-7 Geometric (Exponential) Phase A-7 Linear Phase A-8 Plateau Phase A-8 Amplification Plot exporting as a graphic file B-8 exporting data as a text file B-9 setting the baseline 6-10 setting the threshold 6-11 visualizing outliers 6-12 analyzing absolute quantification data 6-7 to 6-14 allelic discrimination data 5-8 to 5-15 background data 7-16 dissociation curve data 6-20 to 6-24 pure dye data 7-20 applying detector tasks 4-11 detectors to a plate document 4-8 markers to a plate document 4-10 sample names 4-19 archiving SDS files 7-46 assay development guidelines absolute quantification C-2 to C-4, C-6 allelic discrimination C-2 to C-5 attention words, definitions 1-2 automation accessory components 7-27 fixed-position bar code reader See fixed-position bar code reader plate handler, See plate handler Index-1
A(continued) Automation Controller software about 2-14, 4-34 adding plates to the plate queue 4-35 configuring for operation 4-37 ejecting a plate 4-38 launching 4-34 monitoring instrument progress 4-38 removing plates from the plate queue 4-35 starting the plate queue 4-38 stopping the plate queue 4-38 B background run 7-13 to 7-16 about 7-13 constructing a background plate 7-15 creating a plate document 7-14 extracting 7-16 preparing a background plate 7-15 troubleshooting 8-8 when to perform 7-13 bar code information entering into a plate document 3-19, 4-19 bar code readers fixed position, See fixed-position bar code reader hand held, See hand-held bar code reader baseline about A-10 configuring value for automatic analysis 6-8 setting manually 6-10 beam splitter See instrument, optics system Block readout (from the Real Time tab) 4-25 bold text, convention 3-4 C calibrating the 7900HT instrument adjusting the plate-sensor switch 7-28 aligning the fixed-position bar code reader 7-40 aligning the plate handler 7-32 performing background run 7-13 performing pure dye (spectral) run 7-17 CAUTION attention word, definition 1-2 changing gripper finger pads 7-43 pane, view, and plot sizes 3-15 sample block module 7-4 charged coupled device array See instrument, optics system checklists absolute quantification 6-7 allelic discrimination 5-8 dissociation curve 6-20 plate document setup absolute quantification 4-3 allelic discrimination 4-4 dissociation curve 4-4 chemical safety 1-3 Index-2 chemistry non-optimized 8-5 SYBR Green A-3 TaqMan A-2 troubleshooting 8-4 to 8-7 cleaning gripper finger pads 7-43 sample block wells 7-12 closing instrument tray from the Automation Controller software 4-38 from the SDS software 4-27 plate documents 3-14 Zymark Twister software 7-39 comments adding to a detector 4-7 adding to a plate document 4-19 computer about 2-7 hard drive partitions 2-7 maintaining 7-46 minimum system requirements 2-7 troubleshooting 8-14 turning ON 3-5 configuring the 7900 instrument for 9600 emulation 4-14 consumables 384-Well Optical Reaction Plates D-3 96-Well Optical Reaction Plates D-3 improper or damaged plastics 8-7 Optical Adhesive Covers D-3 Optical Cap Strips D-3 writing on reaction plates 8-6 contamination decontaminating the sample block 7-11 fluorescent, common sources 8-6 isolating on the sample block module 8-8 contextual menus, using 3-20 copying detectors to a plate document 4-8 markers to a plate document 4-10 Cover readout (from the Real Time tab) 4-25 creating detectors 4-7 markers 4-9 plate documents 3-12, 4-6 for running background plates 7-14 for running custom pure dyes 7-22 for running pure dye plates 7-18 from a template 4-18, 4-32 C T ,Seethreshold cycle custom pure dyes adding to the pure dye set 7-21 to 7-23 creating a custom pure dye plate 7-21 customer support, See technical support cycle set, adding to a method 4-15
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ABI PRISM ® 7900HT Sequence Detect
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© Copyright 2001, Applied Biosyste
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iv Section:PlateDocumentSetup......
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vi A Theory of Operation Fluorescen
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Attention Words and Warning Labels
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About Waste Profiles A waste profil
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Safe Instrument Use Before Operatin
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Product Overview 2 In This Chapter
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Section: Getting to Know the Hardwa
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Interchangeable Thermal Cycler Bloc
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Computer Description The computer c
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Zymark Twister Microplate Handler D
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Instrument Connections Electrical C
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Section: Getting to Know the Softwa
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Managing Sequence Detection System
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Getting Started 3 In This Chapter T
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Using the SDS Software Online Help
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Turning on the ABI PRISM 7900HT Seq
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Using the SDS Software Workspace La
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Using the General Toolbar Using the
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Basic Software Skills Tutorial Abou
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Exercise 3: Opening a Plate Documen
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Lesson 2: Viewing and Resizing Pane
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Exercise 2: Selecting Multiple Well
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Lesson 4: Using the Hand-Held Bar C
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Using SDS Plate Documents Using Mul
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Run Setup and Basic Operation 4 In
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Setup Checklists Experiments/Runs P
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Section: Plate Document Setup In Th
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Step 2 - Applying Detectors and Mar
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Creating an Allelic Discrimination
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Step 3 - Configuring the Plate Docu
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Step 4 - Programming the Plate Docu
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To create a method for the absolute
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Step 5 - Saving the Plate Document
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Step 7 - Applying Sample and Plate
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Section: Running an Individual Plat
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Preparing and Running a Single Plat
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Operating the 7900HT Instrument Usi
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After the Run Analyzing the Run Dat
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Section: Running Multiple Plates Us
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Adding a Plate Document to the Plat
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To create plate documents from a te
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Adding Plates to the Plate Queue Re
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Loading Plates To load plates onto
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End-Point Analysis 5 In This Chapte
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Section: Allelic Discrimination In
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Algorithmic Manipulation of Raw All
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Before You Begin Using SDS Online H
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Analyzing a Completed Allelic Discr
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Calling Allele Types To call allele
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Scrutinizing the Allele Calls To an
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After the Analysis Changing the Pla
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Real-Time Runs on the 7900HT Instru
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Overview About Absolute Quantificat
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Before You Begin Using SDS Online H
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Analyzing the Run Data Configuring
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Setting the Baseline and Threshold
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Eliminating Outliers For any PCR, e
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Viewing the Standard Curve 6-14 Rea
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6-16 Real-Time Analysis
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Overview About Dissociation Curve A
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Analysis Checklist WhereYouArein th
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Determining T m Values for the Anal
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After the Analysis Changing the Pla
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Recommended Maintenance Schedule Ma
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Replacing the Sample Block When to
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7-6 System Maintenance To remove th
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7-8 System Maintenance To replace t
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7-10 System Maintenance To replace
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Cleaning the Sample Block Wells 7-1
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Prepare a Background Plate Document
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Extracting the Background 7-16 Syst
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Materials Required The following ma
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Extracting Pure Dye Information fro
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Constructing a Custom Pure Dye Plat
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Verifying Instrument Performance Us
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Preparing and Running an RNase P Pl
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Adjusting the Sensitivity of the Pl
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Testing the Adjustment 7-30 System
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Aligning the Plate Handler When to
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7-34 System Maintenance To align th
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Re-checking the Input Stack 1 7-36
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Defining the Positions of the Remai
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Aligning the Fixed-Position Bar Cod
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7-42 System Maintenance To position
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7-44 System Maintenance
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General Computer Maintenance Mainte
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Maintaining the SDS software Admini
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Troubleshooting Table 8-2 Troublesh
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Low Precision or Irreproducibility
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Writing on the Reaction Plates Fluo
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Background Runs Background Troubles
Page 189 and 190: Pure Dye Runs Pure Dye Troubleshoot
Page 191 and 192: 8-12 Troubleshooting Troubleshootin
Page 193 and 194: Software and 7900HT Instrument Trou
Page 195 and 196: 8-16 Troubleshooting Troubleshootin
Page 198: User Bulletins 9 9 About This Chapt
Page 201 and 202: Fluorescent-Based Chemistries Funda
Page 203 and 204: Fluorescence Detection and Data Col
Page 205 and 206: Normalization of Reporter Signals A
Page 207 and 208: Determining Initial Template Concen
Page 209 and 210: Calculating Threshold Cycles A-10 T
Page 212 and 213: Importing and Exporting Plate Docum
Page 214 and 215: Configuring the Setup Table File wi
Page 216 and 217: About the Setup Table File Format S
Page 218 and 219: Setup Table Elements (continued) Nu
Page 220 and 221: Exporting Plate Document Data Expor
Page 222 and 223: Designing TaqMan Assays C In This A
Page 224 and 225: Design Probes and Primers The follo
Page 226 and 227: Design Tips for Allelic Discriminat
Page 228 and 229: Kits, Reagents and Consumables D In
Page 230 and 231: Consumables and Disposables The ABI
Page 232: TaqMan Pre-Developed Assays and Rea
Page 236: Contacting Technical Support F Serv
Page 239: G-2 Limited Warranty Statement No a
Page 243 and 244: I(continued) installing plate adapt
Page 245 and 246: Q quantifying probes and primers C-
Page 248 and 249: Headquarters 850 Lincoln Centre Dri
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