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

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Getting Started 3 In This Chapter This chapter discusses the following topics: 3 Topic See Page Getting Started 3-2 About This Manual 3-3 Turning on the ABI Prism 7900HT Sequence Detection System 3-5 Using the SDS Software Workspace 3-7 BasicSoftwareSkillsTutorial 3-11 Using SDS Plate Documents 3-21 Getting Started 3-1
Getting Started Before You Begin If this is your first time using the ABI PRISM ® 7900HT Sequence Detection System, consider completing the “Basic Software Skills Tutorial” on page 3-11 before continuing. The tutorial will provide you with the fundamental knowledge required to operate the SDS software and will teach you time-saving techniques to allow you to use it quickly and efficiently. Procedure Quick Reference 3-2 Getting Started The following table contains a list of major procedures described within this manual. Procedure See Page Turning on the ABI PRISM 7900HT Sequence Detection System Setting Up and Running SDS Experiments 3-5 Creating an SDS plate document 4-6 Running an individual SDS plate document 4-21 Running batches of SDS plate documents (using the automation accessory) Stopping a run in progress 4-29 ♦ From the SDS software 4-26 ♦ From the Automation Controller Software Ejecting a plate 4-38 ♦ From the SDS software 4-27 ♦ From the Automation Controller Software 4-38 Analyzing Run Data Analyzing an allelic discrimination run 5-3 Analyzing an absolute quantification run 6-3 Analyzing a dissociation curve (melting curve) run Maintaining the 7900HT Instrument 6-17 Changing the 7900HT Plate Adapter 7-9 Replacing the Sample Block 7-4 Decontaminating the Sample Block 7-11 Performing a Background Run 7-13 Performing a Pure Dye Run 7-17 Adding Custom Dyes to the Pure Dye Set 7-21 Verifying Instrument Performance Using a TaqMan RNase P Plate Maintaining the Automation Accessory 7-24 a Adjusting the Sensitivity of the Plate Sensor Switch 7-28 Aligning the Plate Handler 7-32 Aligning the Fixed-Position Bar Code Reader 7-40 Cleaning and Replacing Gripper Finger Pads 7-43 a. The automation accessory includes the Zymark® Twister Microplate Handler and the fixed-position bar code reader. See “Instrument Components” on page 2-3 for more information.
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 22 and 23: Computer Description The computer c
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 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
Page 86 and 87:
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
Page 104 and 105:
Scrutinizing the Allele Calls To an
Page 106:
After the Analysis Changing the Pla
Page 109 and 110:
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
Page 131 and 132:
After the Analysis Changing the Pla
Page 133 and 134:
Recommended Maintenance Schedule Ma
Page 135 and 136:
Replacing the Sample Block When to
Page 137 and 138:
7-6 System Maintenance To remove th
Page 139 and 140:
7-8 System Maintenance To replace t
Page 141 and 142:
7-10 System Maintenance To replace
Page 143 and 144:
Cleaning the Sample Block Wells 7-1
Page 145 and 146:
Prepare a Background Plate Document
Page 147 and 148:
Extracting the Background 7-16 Syst
Page 149 and 150:
Materials Required The following ma
Page 151 and 152:
Extracting Pure Dye Information fro
Page 153 and 154:
Constructing a Custom Pure Dye Plat
Page 155 and 156:
Verifying Instrument Performance Us
Page 157 and 158:
Preparing and Running an RNase P Pl
Page 159 and 160:
Adjusting the Sensitivity of the Pl
Page 161 and 162:
Testing the Adjustment 7-30 System
Page 163 and 164:
Aligning the Plate Handler When to
Page 165 and 166:
7-34 System Maintenance To align th
Page 167 and 168:
Re-checking the Input Stack 1 7-36
Page 169 and 170:
Defining the Positions of the Remai
Page 171 and 172:
Aligning the Fixed-Position Bar Cod
Page 173 and 174:
7-42 System Maintenance To position
Page 175 and 176:
7-44 System Maintenance
Page 177 and 178:
General Computer Maintenance Mainte
Page 179 and 180:
Maintaining the SDS software Admini
Page 181 and 182:
Troubleshooting Table 8-2 Troublesh
Page 183 and 184:
Low Precision or Irreproducibility
Page 185 and 186:
Writing on the Reaction Plates Fluo
Page 187 and 188:
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 and 240:
G-2 Limited Warranty Statement No a
Page 241 and 242:
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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