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7900HT
Applied Biosystems 7900HT User Manual
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DRAF
T
September 1,
2004 11:39 am, CH_Run
.fm
Step
7
–
Creating a
Plate
Document from the T
emplate
Applied Biosystems 7900HT Fast Real-Time PCR Syst
em and SDS Enterprise
Da
tabase User Guide
3-27
4.
Conf
igure th
e new plate document with sample names
and plate infor
mation as
explained on
pa
ge
3-28
.
110
112
Table of Contents
Table of Contents
3
How to Use this Guide
11
Preface
11
How to Obtain more Information
12
How to Obtain Services and Support
12
Safety and Emc Compliance Information
13
Safety and EMC Compliance Information
14
Safety Conventions Used in this Document
14
Symbols on Instruments
15
Safety Labels on Instruments
16
General Instrument Safety
17
Chemical Safety
18
Chemical Waste Safety
19
Electrical Safety
20
Biological Hazard Safety
21
Laser Safety
21
Safety
21
Physical Hazard Safety
21
Bar Code Scanner Laser Safety
22
Safety and Electromagnetic Compatibility (EMC) Standards
23
Workstation Safety
23
1 Product Overview 1
25
Chapter 1 Product Overview
26
System Overview
26
Section 1.1 Getting to Know the Hardware
27
7900HT Instrument
28
Computer
30
Bar Code Readers
31
Zymark Twister Microplate Handler
32
Compatible Consumables
33
Instrument Connections
34
Section 1.2 Getting to Know the Software
37
Software Components
38
SDS Software Related Files and Formats
39
Managing Sequence Detection System Data
41
Section 1.3 SDS Enterprise Database
43
About the SDS Enterprise Database Feature
46
About the SDS Enterprise Database Software Suite
49
Database Modules for Large-Scale Analysis
49
Database Management Utilities
50
Database Design and Information Management
51
Supporting API Documentation
52
September 1, 2004 11:38 Am, Ch_Overview.fm
52
2 Getting Started 2
53
Chapter 2 Getting Started
54
Powering on the 7900HT Instrument
56
Getting Started
56
Using the SDS Software
59
Basic Software Skills Tutorial
62
Notes for Database Users
63
Lesson 1: Using Plate Documents
64
Lesson 2: Viewing and Resizing Panes
73
Lesson 3: Using the Plate Grid
75
Lesson 4: Using the Hand-Held Bar Code Reader
79
Lesson 5: Using Contextual Menus
80
Lesson 6: Using Keyboard Shortcuts
80
Using SDS Plate Documents
81
September 1, 2004 11:38 Am, Ch_Getstart.fm
81
3 Preparing a Run 3
85
Chapter 3 Preparing a Run
86
Notes for Database Users
86
Notes for Database Users
87
Before You Begin
88
Workflow Overview
89
Quick Review: Powering on the 7900HT Instrument
92
Step 1 - Creating a Plate Document
93
Step 2 - Applying Detectors and Markers
95
Step 3 - Configuring the Plate Document with Tasks
100
Step 4 - Setting the Passive Reference and Omitting Wells
102
Step 5 - Programming the Plate Document Method
103
Step 6 - Saving the Plate Document as a Template
108
Step 7 - Creating a Plate Document from the Template
110
Step 8 - Applying Sample and Plate Information
112
Step 9 - Running the Plate on the 7900HT Instrument
113
4 Operating the Instrument 4
115
Chapter 4 Operating the Instrument
116
Notes for Database Users
116
Before You Begin
118
Section 4.1 Consumable Preparation
119
Preventing Contamination
120
Compatible Consumables
120
Preparing Optical Plates for Use
122
Preparing Taqman Low Density Arrays for Use
124
About the Low Density Arrays
124
About the Centrifuge System
126
About the Sealer
128
Loading the Taqman Low Density Arrays
128
Centrifuging the Taqman Low Density Arrays
130
Sealing the Taqman Low Density Arrays
133
Section 4.2 Running an Individual Plate
137
Saving the Plate Document
138
Running a Single Plate (Using the SDS Software)
139
After the Run
143
Section 4.3 Automated Operation
145
Operating the Software with an SDS Enterprise Database
146
Operating the Software Without an SDS Enterprise Database
148
Adding a Plate Document to the Plate Queue (Using the SDS Software)
149
Creating Plate Documents Using the Template Batch Utility
150
Starting and Configuring the Automation Controller Software for Operation
153
Running Plates Using the Automation Controller Software
155
Loading Plates Onto the Plate Handler
155
Running the Instrument
157
After the Run
158
5 Analyzing End-Point Data 5
159
Chapter 5 Analyzing End-Point Data
160
End-Point Runs on the 7900HT Instrument
160
Notes for Database Users
161
Section 5.1 Allelic Discrimination
163
Default Chapter
164
Overview
164
Before You Begin
167
Analysis Checklist
168
Opening the Run Data
169
Analyzing an Allelic Discrimination Run
170
Calling and Scrutinizing Allelic Discrimination Data
171
After the Analysis
176
Chapter 6 Analyzing Real-Time Data
180
Notes for Database Users
180
Real-Time Runs on the 7900HT Instrument
182
Section 6.1 Absolute Quantification
183
Overview
184
Before You Begin
186
Analysis Checklist
187
Opening the Run Data
188
Analyzing the Data
189
Viewing Results
191
After the Analysis
192
Section 6.2 Relative Quantification
193
Overview
194
Algorithmic Manipulation of Raw Data
195
Automatic Outlier Removal
197
Essential Experimental Components
198
Getting Started
199
Analysis Checklist
200
Overview
200
Creating the Study
201
Options for Analyzing Relative Quantification Data
201
Analyzing the Study
204
About the Analysis Settings
204
Specifying the Analysis Settings
207
Analyzing the Study Data
208
Analyzing the Data
208
Viewing Results
209
After the Analysis
213
Section 6.3 Dissociation Curve Analysis
215
Overview
216
Before You Begin
217
Analysis Checklist
218
Overview
218
Analyzing the Run Data
219
Opening the Run Data
219
Determining T Values for the Analyzed Run
220
Values for the Analyzed Run
220
After the Analysis
222
Section 6.4 Procedure Reference
223
Setting the Baseline and Threshold Values
224
Eliminating Outlying Amplification
227
After the Analysis
230
September 1, 2004 11:39 Am, Ch_Real-Time.fm
230
7 Maintaining the Instrument 7
233
Chapter 7 Maintaining the Instrument
234
Notes for Database Users
234
Recommended Maintenance Schedule
236
Section 7.1 Maintaining the 7900HT Instrument
237
Replacing the Sample Block
238
Changing the Plate Adapter
244
Decontaminating the Sample Block
246
Performing a Background Run
248
Preparing the Background Plate or Taqman Low Density Array
249
Creating a Plate Document for the Background Run
249
Running the Prepared Background Plate or Taqman Low Density Array
250
Analyzing the Background Data
251
Performing a Pure Dye Run
252
Preparing the Pure Dye Plates or Cards
254
Preparing a Plate Document for a Pure Dye Plate or Card
254
Running the Prepared Pure Dye Plate or Card
256
Analyzing the Pure Dye Run
257
Adding Custom Dyes to the Pure Dye Set
259
Verifying Instrument Performance
262
Section 7.2 Maintaining the Plate Handler
267
Automation Accessory Components and Stack Positions
268
Adjusting the Sensitivity of the Plate Sensor Switch
269
Aligning the Plate Handler
273
Aligning the Fixed-Position Bar Code Reader
281
Cleaning and Replacing Gripper Finger Pads
284
Section 7.3 Maintaining the Computer and Software
285
General Computer Maintenance
286
Maintaining the SDS Software
287
8 Troubleshooting 8
289
Chapter 8 Troubleshooting
290
Troubleshooting Table
290
Low Precision or Irreproducibility
293
Low Precision or Irreproducibility
295
Background Runs
297
Pure Dye Runs
299
Real-Time Runs (Quantitative PCR and Dissociation Curves)
300
End-Point Runs (Allelic Discrimination)
301
Software and 7900HT Instrument
302
Zymark Twister Microplate Handler and Fixed-Position Bar Code Reader
305
Taqman Low Density Array
306
SDS Enterprise Database
308
September 1, 2004 11:39 Am, Ch_Trouble.fm
308
Software Reference a
309
Appendix A Software Reference
310
Importing Plate Document Setup Table Files
310
Setup Table Files
312
File Version
313
Plate Characteristics
313
Plate Size
313
Plate ID
313
Detector Definitions
314
Number of Detectors
314
Detectors List Header
314
Detectors List
315
Marker Definitions
316
Number of Markers (Allelic Discrimination Only
316
Markers List Header (Allelic Discrimination Only
316
Markers List (Allelic Discrimination Only
317
Well-Detector Information
318
10. Well-Detector List Header
318
11. Well-Detector Definition List
318
Well-Marker Information
320
Well-Marker List Header (Allelic Discrimination Only
320
Well-Marker Definition List (Allelic Discrimination Only
320
In this Appendix
320
Setup Table Files
320
Example Setup Table Files
322
Exporting Graphics
324
Exporting Plate Document Data
324
Operating the SDS Software from a Command Line
326
Using the Search Tool
328
Connecting SDS Software to the Database
330
Appendix B Designing Taqman Reagent-Based Assays
334
Assay Development Guidelines
334
Design Tips for Allelic Discrimination Assays
337
Design Tips for Quantitative PCR Assays
338
Kits, Reagents, and Consumables C
339
Appendix C Kits, Reagents, and Consumables
340
Interchangeable Sample Block Modules and Accessories
340
Consumables and Disposables
341
Instrument Maintenance and Verification
343
Custom Oligonucleotide Synthesis
344
Appendix D Theory of Operation
348
Taqman Pre-Developed Assays and Reagents
344
Fluorescent-Based Chemistries
348
Real-Time Data Analysis
350
Comparative C Method of Relative Quantification
354
Appendix E Limited Warranty Statement
357
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Getting Started Guide
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Applied Biosystems 7900HT Specifications
General
Brand
Applied Biosystems
Model
7900HT
Category
Laboratory Equipment
Language
English
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