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

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Computer Description The computer coordinates the operation of the Sequence Detection instrument, automation module, and the bar code readers via the SDS software. The figure below illustrates the general configuration of the computer supplied with the ABI PRISM 7900HT Sequence Detection System. System Requirements Hard Drive Partitions GR2009 Monitor power button Computer power button IMPORTANT The following requirements are valid for Version 2.0 of the SDS software and may change with future revisions of the 7900HT instrument software and firmware. Check the release notes accompanying your version of the SDS software for updates. To run the SDS software and/or to operate the ABI PRISM 7900HT Sequence Detection System, a computer must meet the following minimum requirements: Component Minimum Requirement Processor Intel Pentium II processor, 400 MHz or faster Memory 256 MB RAM Hard Drive Minimum 25 GB available hard disk space Additional Drives CD-ROM drive Operating Systems Microsoft Windows NT 4.0 with Service Pack 6A During installation of the 7900HT instrument, the computer hard drive was partitioned to create the following logical drives: Partition Size (GB) Contains C 2 Operating system files Note Applied Biosystems recommends that you do not install D ≥25 programs to the C drive. The computer will boot faster if the C drive contains only the operating system. ♦ SDS 2.0 Software ♦ Automation Controller Software ♦ Additional Third-Party Software ♦ ABI PRISM SDS Plate Document Files Product Overview 2-7
Bar Code Readers 2-8 Product Overview Description The ABI PRISM 7900HT Sequence Detection System incudes two bar code readers for data entry and plate recognition: ♦ a hand-held bar code reader for scanning plates manually ♦ a fixed-position bar code reader for automated scanning of plates as they are loaded into the instrument (available with automation accessory only) Locations of the BarCodeReaders Using the BarCodeReaders Both bar code readers use a 488 nM laser to scan plates and are capable of reading Code 128 (alpha-numeric), which supports 128 ASCII characters. The following figure illustrates the locations of the bar code readers in the system. 1 Fixed-Position Bar Code Reader Hand-Held Bar Code Reader (Shown with cover removed) 1 GR2018 ! WARNING LASER HAZARD. Exposure to direct or reflected laser light can burn the retina and leave permanent blind spots. Never look into the laser beam. Remove jewelry and anything else that can reflect the beam into your eyes. Protect others from exposure to the beam. 2 ~ Splitter To computer keyboard port ~ ~ To keyboard For directions on... See Page Using the Hand-Held Bar Code Reader 3-19 Aligning the Fixed-Position Bar Code Reader 7-40 2 GR2015 GR2009
Page 1 and 2: ABI PRISM ® 7900HT Sequence Detect
Page 3 and 4: © Copyright 2001, Applied Biosyste
Page 5 and 6: iv Section:PlateDocumentSetup......
Page 7 and 8: vi A Theory of Operation Fluorescen
Page 9 and 10: Attention Words and Warning Labels
Page 11 and 12: About Waste Profiles A waste profil
Page 13 and 14: Safe Instrument Use Before Operatin
Page 16 and 17: Product Overview 2 In This Chapter
Page 18 and 19: Section: Getting to Know the Hardwa
Page 20 and 21: Interchangeable Thermal Cycler Bloc
Page 24 and 25: Zymark Twister Microplate Handler D
Page 26 and 27: Instrument Connections Electrical C
Page 28 and 29: Section: Getting to Know the Softwa
Page 30 and 31: Managing Sequence Detection System
Page 32 and 33: Getting Started 3 In This Chapter T
Page 34 and 35: Using the SDS Software Online Help
Page 36 and 37: Turning on the ABI PRISM 7900HT Seq
Page 38 and 39: Using the SDS Software Workspace La
Page 40 and 41: Using the General Toolbar Using the
Page 42 and 43: Basic Software Skills Tutorial Abou
Page 44 and 45: Exercise 3: Opening a Plate Documen
Page 46 and 47: Lesson 2: Viewing and Resizing Pane
Page 48 and 49: Exercise 2: Selecting Multiple Well
Page 50 and 51: Lesson 4: Using the Hand-Held Bar C
Page 52 and 53: Using SDS Plate Documents Using Mul
Page 54 and 55: Run Setup and Basic Operation 4 In
Page 56 and 57: Setup Checklists Experiments/Runs P
Page 58 and 59: Section: Plate Document Setup In Th
Page 60 and 61: Step 2 - Applying Detectors and Mar
Page 62 and 63: Creating an Allelic Discrimination
Page 64 and 65: Step 3 - Configuring the Plate Docu
Page 66 and 67: Step 4 - Programming the Plate Docu
Page 68 and 69: To create a method for the absolute
Page 70 and 71: Step 5 - Saving the Plate Document
Page 72 and 73:
Step 7 - Applying Sample and Plate
Page 74 and 75:
Section: Running an Individual Plat
Page 76 and 77:
Preparing and Running a Single Plat
Page 78 and 79:
Operating the 7900HT Instrument Usi
Page 80 and 81:
After the Run Analyzing the Run Dat
Page 82 and 83:
Section: Running Multiple Plates Us
Page 84 and 85:
Adding a Plate Document to the Plat
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To create plate documents from a te
Page 88 and 89:
Adding Plates to the Plate Queue Re
Page 90 and 91:
Loading Plates To load plates onto
Page 92 and 93:
End-Point Analysis 5 In This Chapte
Page 94 and 95:
Section: Allelic Discrimination In
Page 96 and 97:
Algorithmic Manipulation of Raw All
Page 98 and 99:
Before You Begin Using SDS Online H
Page 100 and 101:
Analyzing a Completed Allelic Discr
Page 102 and 103:
Calling Allele Types To call allele
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Scrutinizing the Allele Calls To an
Page 106:
After the Analysis Changing the Pla
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Real-Time Runs on the 7900HT Instru
Page 111 and 112:
Overview About Absolute Quantificat
Page 113 and 114:
Before You Begin Using SDS Online H
Page 115 and 116:
Analyzing the Run Data Configuring
Page 117 and 118:
Setting the Baseline and Threshold
Page 119 and 120:
Eliminating Outliers For any PCR, e
Page 121 and 122:
Viewing the Standard Curve 6-14 Rea
Page 123 and 124:
6-16 Real-Time Analysis
Page 125 and 126:
Overview About Dissociation Curve A
Page 127 and 128:
Analysis Checklist WhereYouArein th
Page 129 and 130:
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
Page 151 and 152:
Extracting Pure Dye Information fro
Page 153 and 154:
Constructing a Custom Pure Dye Plat
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Verifying Instrument Performance Us
Page 157 and 158:
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
Page 179 and 180:
Maintaining the SDS software Admini
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Troubleshooting Table 8-2 Troublesh
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Low Precision or Irreproducibility
Page 185 and 186:
Writing on the Reaction Plates Fluo
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Background Runs Background Troubles
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Pure Dye Runs Pure Dye Troubleshoot
Page 191 and 192:
8-12 Troubleshooting Troubleshootin
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Software and 7900HT Instrument Trou
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8-16 Troubleshooting Troubleshootin
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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
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TaqMan Pre-Developed Assays and Rea
Page 236:
Contacting Technical Support F Serv
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G-2 Limited Warranty Statement No a
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A(continued) Automation Controller
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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