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Applied Biosystems 3500 Manuals
Manuals and User Guides for Applied Biosystems 3500. We have
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Applied Biosystems 3500 manual available for free PDF download: User Manual
Applied Biosystems 3500 User Manual (326 pages)
Genetic Analyzer
Brand:
Applied Biosystems
| Category:
Measuring Instruments
| Size: 6.77 MB
Table of Contents
Table of Contents
3
CHAPTER 1 Instrument and Software Description
14
Instrument and Software Description
14
Overview
14
Precautions for Use
15
Instrument Interior Components
15
Instrument Parts and Functions
16
Instrument Front Panel Indicators
17
Instrument and Computer Requirements
17
Windows ™ Software Requirements
17
Antivirus Software Requirements
17
Other Software
17
Instrument Firmware
18
Theory of Operation
18
Preparing Samples
18
Preparing the Instrument
18
During a Run
18
Results
19
Materials for Routine Operation
19
Instrument Consumables Handling, Usage Limits, and Expiration
19
Buffers
19
Polymer
20
Conditioning Reagent
21
Capillary Arrays
21
Hi-DI ™ Formamide
22
Important Notice Regarding Use of Consumables that Exceed Supported Limits
22
Overview of the 3500 Series Data Collection Software 3.1
23
About the Software
23
Dashboard
23
Workflow
24
Maintenance Workflow
25
Library Workflow
25
SAE Menu
26
Tools Menu
26
Manage Menu
26
Preferences Menu
27
Help Menu
27
Use the Software Without an Instrument
27
CHAPTER 2 Start the System
28
Workflow
28
Start the Computer and Instrument
29
Start the Software
30
Step One: Start the Server Monitor
30
Step Two: Start the 3500 Series Data Collection Software 3.1
31
Step Three: Log in
31
Check System Status in the Dashboard
32
Check Calendar Reminders
32
Check Consumables Status
33
How the Polymer Sample and Injection Counters Calculate Usage
34
Check for Leaks and Spills
34
Check Buffer Fill Levels
34
Replenish Consumables
35
Ensure Proper Installation of CBC Septa
35
Set Preferences (Optional)
36
Overview
36
System Preferences
37
User Preferences
37
CHAPTER 3 Set up and Run
40
Setup Workflow
41
Prepare the Instrument
41
Create or Import a Plate
42
About Plate Templates
42
Create a Plate from a Template
42
Import a Plate
44
Assign Plate Contents
44
Access the Assign Plate Contents Screen
45
Name Samples and Assign Sample Types in the Plate View
47
Assign Assay, File Name Convention, and Results Group in the Plate View
49
How File Location in File Name Conventions and Results Groups Work
50
Print the Plate Layout
50
Prepare and Load Sample Plates
50
Capillary-To-Plate Mapping
51
Allelic Ladder Run Requirements
51
Results Group for One Allelic Ladder Per Run Folder
52
Prepare Sample Plates
52
Prepare the Plate Assembly
53
Load the Plate in the Instrument
56
Link the Plate
57
Quick Start a Run
58
Load Plates for Run and Create the Injection List
59
Link a Plate (if a Plate Is Not Linked)
61
Link a Plate from the Recent Plates or Recent Runs Tab
62
Review and Modify the Injection List in Preview Run
62
Start the Run from Preview Run
64
Monitor the Run
65
Check Sequence or Sample Quality and Re-Inject Samples
67
Check Sequence or Sample Quality
67
Re-Inject Samples from the Monitor Run Screen
69
If You Select a Protocol Other than the Original
70
How Re-Injections Are Displayed in the Plate View
70
Re-Inject HID Allelic Ladder Samples
71
Review Completed Injections in Review Results
72
Pause, Resume, or Stop a Run
72
Pause and Resume
72
Abort or Terminate
72
More Features in Assign Plate Contents
73
Name Samples in the Plate View
73
Customize the Plate View
74
View the Capillary-To-Plate Map
75
Use the Table View
75
Sort by One or Multiple Columns
76
Customize a Table
76
Add Assays, File Name Conventions, and Results Groups to a Plate
77
Create a Plate Import Template
77
Create a Plate Import File
78
Edit a Plate
79
Import and Export a Plate
79
Create a Plate Template
79
Specify the Default Plate Type for the Open Plate Dialog Box
80
Save Electronic Version of Reports
80
More Features in Monitor Run
80
Review the Instrument Run Views
80
Array View
81
Sample View
81
EPT View
81
CHAPTER 4 Review Sequencing Results
82
Workflow
82
Access the View Sequencing Results Screen
82
Review Results for the Currently Running Sequencing Plate
83
Review Previously Run Sequencing Samples
84
Review Sequence Quality
84
Review Traces
86
Display Thumbnails
87
Understand Quality Values (Qvs)
88
Quality Value Ranges
88
Pure Base Versus Mixed Base Qvs
88
Quality Values (QV) and Probability of Error (Pe)
88
Re-Inject Samples from Review Sequencing Results
89
View, Print, and Save (.Pdf) Trace Quality Reports
89
View Trace Reports
89
Report Options
90
Export Sequencing Results
90
Modify Sequence Data
90
CHAPTER 5 Review Fragment/Hid Analysis Results
91
Workflow
91
Access the View Fragment/Hid Results Screen
92
Review Results for the Currently Running Fragment/Hid Analysis Plate
93
Review Previously Run Fragment Analysis/Hid Samples
94
Review Sample Quality
94
Review Normalized Data
96
How Normalization Is Applied
96
Normalization Factor in Secondary Analysis
96
Review Plots
97
Zoom on Data
97
Change Plot Settings
97
Overlay Samples
98
Label Peaks
98
View Thumbnails
99
Rename Samples
99
Sort by One or Multiple Columns
100
Review Sizing
100
Set up the Sizing Table
100
Examine the Size Standard Plot
100
Overlay the Sizing Curve
101
Re-Inject Samples from Review Fragment Results
101
View, Print, and Save (.Pdf) Sample Quality Reports
101
Report Options
101
Export Sizing Results
102
Modify Fragment Analysis or HID Data
102
CHAPTER 6 Run Calibrations and Install Checks
103
Section 6.1 Run Spatial and Spectral Calibrations
104
Run a Spatial Calibration
104
Spatial Calibration Overview
104
When to Perform a Spatial Calibration
104
Perform a Spatial Calibration
104
Run Spatial and Spectral Calibrations
104
Evaluate the Spatial Calibration Profile
105
Example Spatial Profiles
106
Export Spatial Calibration Results
106
View and Print a Calibration Report
107
Save Historical Reports (.Pdf) for Record Keeping
107
Run a Spectral Calibration
107
Spectral Calibration Overview
107
When to Perform a Spectral Calibration
107
Estimated Run Time
108
Prepare for Spectral Calibration
108
Perform a Spectral Calibration
111
Spectral Quality Values and Condition Numbers
113
Evaluate the Spectral Calibration Data
114
What You See During a Spectral Calibration
115
Capillary Information Sharing
116
Example Spectral Calibration Data
118
Export Spectral Calibration Results
119
View and Print a Calibration Report
119
Save Historical Reports (.Pdf) for Record Keeping
120
View the Spectral Calibration History
120
Section 6.2 Run an Install Check
121
Run a Sequencing Install Check
121
When to Perform a Sequencing Install Check
121
Estimated Run Time
121
Prepare for the Sequencing Install Check
121
Run an Install Check
121
Perform a Sequencing Install Check
123
What You See During a Sequencing Install Check
125
Pass/Fail Criteria for the Optional Spectral Calibration
126
Pass/Fail Criteria for the Sequencing Install Check
127
Evaluate Sequencing Install Standard Data
128
Example Sequencing Install Check Results
129
View Previously Run Install Standards
129
View and Print an Install Check Report
130
Save Historical Reports (.Pdf) for Record Keeping
130
Run a Fragment/Hid Install Check
130
When to Perform a Fragment/Hid Install Check
130
Estimated Run Time
130
Prepare for the Fragment/Hid Install Check
130
Perform the Fragment/Hid Install Check
133
What You See During a Fragment Install Check
134
Pass/Fail Criteria for the Fragment/Hid Install Check
135
Evaluate Fragment Install Standard Data
135
Example Fragment Install Standard Results
136
Example HID Install Standard Results
136
View Previously Run Install Standards
136
View and Print an Install Check Report
137
Save Historical Reports (.Pdf) for Record Keeping
137
CHAPTER 7 Manage Library Resources
138
Overview of Libraries
138
Factory-Provided Template and Locked Items
139
General Library Procedures
139
Access Libraries
139
Create a New Entry from a Factory-Provided Template or Locked Entry
140
Delete a Library Entry
140
Edit a Library Entry
140
Import and Export a Library Entry
141
View Audit and E-Signature Histories for Library Entries
141
Sort and Search Library Entries
141
Customize a Table
142
Plates Library
142
Plate Overview
142
Create a New Plate
143
Define Plate Properties
144
Assays Library
144
Assay Overview
144
Create a New Assay
145
Assay Settings
146
File Name Conventions Library
147
File Name Convention Overview
147
Create a New File Name Convention
148
File Name Convention Settings
150
Results Group Library
152
Results Group Overview
152
Allelic Ladder Location (HID Analysis)
152
Create a New Results Group
153
Results Group Settings
155
Results Group Example 1: Store Files by Plate Name
157
Results Group Example 2: Store Re-Injections in Separate Folders
158
Results Group Example 3: Store One Allelic Ladder Per Run Folder
160
Capillary Instruments)
160
Instrument Protocol Library
161
Instrument Protocol Overview
161
Create a New Instrument Protocol
162
Instrument Protocol Settings
163
Dye Sets Library
165
Dye Set Overview
165
Create a New Dye Set
166
Dye Set Settings
167
Create a New Dye Set Using the Anydye Template
168
Size Standards Library
170
Size Standard Overview
170
Normalization Size Standards Provided
171
Create a New Size Standard
171
Modify a Factory-Provided Normalization Size Standard
172
Basecalling Protocols Library (Primary Analysis-Sequencing)
173
Basecalling Protocol Overview
173
Create a New Basecalling Protocol
173
Basecalling Protocol-Analysis Settings
176
Basecalling Protocol-QV Settings
178
Sizecalling Protocols Library (Primary Analysis-Fragment)
178
Sizecalling Protocol Overview
178
Create a New Sizecalling Protocol
179
Sizecalling Protocol-Analysis Settings
181
Sizecalling Protocol-QC Settings
184
QC Protocols Library (Primary Analysis-HID)
185
QC Protocol Overview
185
Create a New QC Protocol
185
QC Protocol-Analysis Settings
187
QC Protocol-QC Settings
190
CHAPTER 8 Use Security, Audit, and E-Sig Functions
191
(SAE Module)
191
Administrators
191
Administrators Overview of System Security Auditing and Electronic Signature
191
Configure the Security System
192
Manage User Accounts
195
Manage Auditing
201
Generate Audit Reports
204
Manage Electronic Signature (E-Sig)
211
Export and Import User Accounts Security Audit and Electronic Signature Settings
217
Users
218
Users Overview of System Security Audit Trail and E-Signature
218
Security
219
Audit
221
Electronic Signature
221
CHAPTER 9 Maintain the Instrument
223
Maintenance Schedule
223
Review Calendar Reminders
223
Daily Instrument Maintenance Tasks
224
Weekly Instrument Maintenance Tasks
225
Monthly Instrument Maintenance Tasks
225
Quarterly Maintenance Tasks
226
Annual Planned Maintenance Tasks
226
As-Needed Instrument Maintenance Tasks
226
Use the Maintenance Calendar
226
Create Calendar Entries
227
View the Planned Maintenance Report
227
Review the Notifications Log
228
Clean the Instrument
229
Install Buffers
229
Install the Anode Buffer Container (ABC)
229
Install the Cathode Buffer Container (CBC)
230
Replenish, Change, Flush, and Store Polymer
232
Precautions for Use
232
Replenish Polymer or Change Polymer Type
232
Store Partially Used Polymer
234
Fill Capillary Array with Fresh Polymer
234
Change and Store a Capillary Array
235
Install or Change the Capillary Array
235
Store a Capillary Array
236
Maintain the Pump
236
Avoiding Damage to the Pump Assembly
236
Remove Bubbles from the Polymer Pump
237
Wash the Pump Chamber and Channels
237
Flush the Water Trap (Pump Trap)
238
Shutdown Move and Reactivate the Instrument
240
Shutdown the Instrument
240
Move and Level the Instrument
241
Reactivate the Instrument
242
Maintain the Computer
242
Back up the Datastore During Software Uninstall
242
Archive, Purge, and Restore Data
243
Monitor Disk Space
245
Manage Software Licenses
246
Create an Email Address for License Activation and Renewal
246
Obtain and Activate a Software License
246
Renew a Software License
248
Service Log and Usage Statistics
249
APPENDIX A Troubleshoot
251
Restart the Instrument and the Computer
251
Instrument Components
252
Instrument Troubleshooting
254
RFID Troubleshooting
258
Error Messages
259
Dashboard Troubleshooting
261
Software Troubleshooting - General
262
Run, Re-Run, or Re-Inject Troubleshooting
264
Data/Electropherogram Troubleshooting
264
Review Results Troubleshooting
267
Link/Load Plate Troubleshooting
269
Assign Plate Contents Troubleshooting
270
Spatial Calibration Troubleshooting
271
Spectral Calibration Troubleshooting
272
Sequencing Install Standard Troubleshooting
274
Fragment/Hid Install Standard Troubleshooting
275
Monitor Run Troubleshooting
276
Audit Troubleshooting
277
Electronic Signature Troubleshooting
277
Manual Commands Troubleshooting
278
Troubleshooting Procedures
278
Run Troubleshooting Utility.bat
278
View the Log Files
278
View Instrument Sensor Details
279
Review Error Message Details
280
Reset the Instrument
280
APPENDIX B Run Modules and Dye Sets
281
Run Modules
281
Dye Sets
284
Sequencing Analysis Dye Sets
284
Fragment Analysis Dye Sets for All Applications
284
HID Analysis Dye Sets
285
APPENDIX C Instrument Specifications
286
Instrument Specifications
286
Environmental Requirements
287
Power and Communication Connections
288
APPENDIX D Catalog Numbers
289
Plates Bases Retainers and Septa
289
Instrument Consumables
290
Sequencing Analysis Reagents and Consumables
290
Fragment and HID Analysis Reagents
291
APPENDIX E Limitations
292
Computer
292
General
292
Calibration and Install Checks
293
Instrument and Consumables
293
Security Audit and E-Sig
293
Review Results
294
APPENDIX F Radio Frequency Identification (RFID) Technology
295
Precautions for Use
295
Function
296
Locations of RFID Read/Write Units
296
Specifications
297
Troubleshooting
298
APPENDIX G Normalization
299
Overview of the Normalization Feature
299
When to Use the Normalization Feature
300
APPENDIX H Safety
301
Symbols on this Instrument
301
Conformity Symbols
302
Safety Alerts on this Instrument
303
Location of Safety Labels on this Instrument
303
Instrument Safety
304
General
304
Physical Injury
304
Electrical Safety
305
Cleaning and Decontamination
305
Laser
306
Safety and Electromagnetic Compatibility (EMC) Standards
306
Safety (Compliance)
306
Emc
307
Environmental Design
307
Radio Compliance
307
Chemical Safety
308
Biological Hazard Safety
309
Customer and Technical Support
310
Documentation and Support
310
Obtaining Support
310
Related Documentation
310
Limited Product Warranty
311
Additional Instrument Symbols
312
Index
313
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