Thermo Scientific Ion Torrent Genexus Integrated Sequencer Manuals

Manuals and User Guides for Thermo Scientific Ion Torrent Genexus Integrated Sequencer. We have 1 Thermo Scientific Ion Torrent Genexus Integrated Sequencer manual available for free PDF download: User Manual

Thermo Scientific Ion Torrent Genexus Integrated Sequencer User Manual (163 pages)

Integrated Sequencer

Brand: Thermo Scientific | Category: Laboratory Equipment | Size: 7 MB

Table of Contents
3
CHAPTER 1 Product Information

8
CHAPTER 2 Before You Begin

23
- Precautions
  23
- Guidelines for Genexus
  24
- Power the Genexus ™ Integrated Sequencer on or off
  25
  - Power on
    25
  - Power off
    26
- Get Started with Genexus ™ Software
  26
  - About the Genexus ™ Software User Interface
    26
  - User-Access Levels
    27
  - System Tracking
    27
  - Request and Sign in to a New Account
    27
  - Sign in
    28
CHAPTER 3 Create and Manage

29
CHAPTER 4 Enter Samples and Libraries

42
CHAPTER 5 Create and Manage Run Plans

55
- Create a Run Plan for a Sample Run
  56
- Create a Run Plan for a Library Run
  63
CHAPTER 6 Dilute the Samples and Load the Sample Plate

68
CHAPTER 7 Load the Sequencer and Start a Run

72
CHAPTER 8 Monitor the Run

84
- View Run Progress on the Instrument
  84
CHAPTER 9 Review Data and Results

85
- Run Results Screen
  86
- Lab Report
  88
  - Download the Lab Report
    89
- View Sequencing Results and Run Metrics
  89
  - Summary of the Sample Results
    91
  - Run Metrics
    92
  - QC Results
    94
  - SNV/INDEL Results
    95
  - Fusion Results
    97
  - CNV Results
    99
  - View Annotation Sources
    101
  - Create and Assign Variant Classifications
    102
  - Filter Results
    102
  - View Oncomine ™ TCR Beta-LR Assay GX Run Results
    105
- Sign off on the Run Results (Manager/ Administrator)
  107
  - Sign off on the Run Results (Manager/ a Dministrator)
    107
- Generate Customized Reports
  108
- Results Files
  109
- Review Coverageanalysis Plugin Results
  111
- Upload Sample Results Files to Ion Reporter ™ Software
  111
  - Software
    111
- Verification Runs
  113
  - View and Sign off on the Verification Run Results (Field Service Engineer)
    114
APPENDIX A Troubleshooting

117
- Genexus ™ Software
  117
- Genexus ™ Integrated Sequencer
  119
APPENDIX B Touchscreen Reference

120
- Touchscreen Icons
  120
- Settings
  121
  - Network Settings
    122
  - Perform a Clean Instrument Operation
    124
  - System Tools
    124
  - Data Management
    129
  - Instrument Settings
    131
APPENDIX C Supplemental Information

134
- Maintain the Sequencer
  134
  - Materials Required
    134
  - Clean or Decontaminate the Sequencer
    134
  - Replace the Genexus
    135
- Quantify FFPE DNA with the Qubit
  135
  - Filter
    135
  - Fluorometer
    135
- Guidelines for Using Custom Assays with the Genexus
  136
  - Integrated Sequencer
    136
- Planning Sequencing Runs for Efficient Use of Consumables
  138
- Configure an Ion Reporter
  139
  - Server Account (Administrator)
    139
  - Tag an Ion Reporter
    140
  - Ionreporteruploader Plugin
    140
- Configure Thermo Fisher (Connect) Accounts (Manager/Administrator)
  141
APPENDIX D Coverageanalysis Plugin in Genexussoftware

143
APPENDIX E Safety

150
- Symbols on this Instrument
  150
  - Standard Safety Symbols
    150
  - Additional Safety Symbols
    152
  - Location of Safety Labels
    152
  - Control and Connection Symbols
    153
  - Conformity Symbols
    153
- Instrument Safety
  154
  - General
    154
  - Physical Injury
    154
  - Electrical Safety
    155
  - Cleaning and Decontamination
    156
  - Instrument Component and Accessory Disposal
    156
- Safety and Electromagnetic Compatibility (EMC) Standards
  156
  - Safety Standards
    157
  - EMC Standards
    157
  - Environmental Design Standards
    158
  - Radio Compliance Standards
    158
- Chemical Safety
  159
- Biological Hazard Safety
  161
APPENDIX F Documentation and Support

162
- Related Documentation
  162
- Customer and Technical Support
  162
- Limited Product Warranty
  162

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Thermo Scientific Ion Torrent Genexus Integrated Sequencer Manuals

Thermo Scientific Ion Torrent Genexus Integrated Sequencer User Manual (163 pages)

Table of Contents

CHAPTER 1 Product Information

CHAPTER 2 Before You Begin

CHAPTER 3 Create and Manage

CHAPTER 4 Enter Samples and Libraries

CHAPTER 5 Create and Manage Run Plans

CHAPTER 6 Dilute the Samples and Load the Sample Plate

CHAPTER 7 Load the Sequencer and Start a Run

CHAPTER 8 Monitor the Run

CHAPTER 9 Review Data and Results

APPENDIX A Troubleshooting

APPENDIX B Touchscreen Reference

APPENDIX C Supplemental Information

APPENDIX D Coverageanalysis Plugin in Genexussoftware

APPENDIX E Safety

APPENDIX F Documentation and Support

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