Applied Biosystems 3500xL Manuals

Manuals and User Guides for Applied Biosystems 3500xL. We have 1 Applied Biosystems 3500xL manual available for free PDF download: User Manual

Applied Biosystems 3500xL User Manual (326 pages)

Genetic Analyzer

Brand: Applied Biosystems | Category: Measuring Instruments | Size: 6 MB

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
- Check System Status in the Dashboard
  32
- Set Preferences (Optional)
  36
  - Overview
    36
  - System Preferences
    37
  - User Preferences
    37
CHAPTER 3 Set up and Run

40
CHAPTER 4 Review Sequencing Results

82
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
CHAPTER 7 Manage Library Resources

138
- Overview of Libraries
  138
  - Factory-Provided Template and Locked Items
    139
- General Library Procedures
  139
- 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
- Results Group Library
  152
- 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
- Basecalling Protocols Library (Primary Analysis-Sequencing)
  173
- Sizecalling Protocols Library (Primary Analysis-Fragment)
  178
- 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
- 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
- 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
- Change and Store a Capillary Array
  235
  - Install or Change the Capillary Array
    235
  - Store a Capillary Array
    236
- Maintain the Pump
  236
- 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
- Manage Software Licenses
  246
- 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
APPENDIX C Instrument Specifications

286
- Instrument Specifications
  286
- Environmental Requirements
  287
- Power and Communication Connections
  288
APPENDIX D Catalog Numbers

289
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

Applied Biosystems Categories

Laboratory Equipment Measuring Instruments Bicycle Accessories Software Control Unit

More Applied Biosystems Manuals

Applied Biosystems 3500xL Manuals

Applied Biosystems 3500xL User Manual (326 pages)

Table of Contents

CHAPTER 1 Instrument and Software Description

CHAPTER 2 Start the System

CHAPTER 3 Set up and Run

CHAPTER 4 Review Sequencing Results

CHAPTER 5 Review Fragment/Hid Analysis Results

CHAPTER 6 Run Calibrations and Install Checks

CHAPTER 7 Manage Library Resources

CHAPTER 8 Use Security, Audit, and E-Sig Functions

CHAPTER 9 Maintain the Instrument

APPENDIX A Troubleshoot

APPENDIX B Run Modules and Dye Sets

APPENDIX C Instrument Specifications

APPENDIX D Catalog Numbers

APPENDIX E Limitations

APPENDIX F Radio Frequency Identification (RFID) Technology

APPENDIX G Normalization

APPENDIX H Safety

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