Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer - Page 209

Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer

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Example fragment analysis run report

Appendix C Dye calibration and install standard checks

Perform an install run

C

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

209

Table of Contents

Default Chapter3
- Table of Contents3
CHAPTER 1 Product Information12
- Instrument Overview13
- Parts of the Instrument14
  - Instrument Status Indicator15
- Seqstudio ™ Genetic Analyzer Consumables15
- Software Features22
- Seqstudio ™ Plate Manager Overview24
  - Computer and Operating System Options25
  - Recommended Browsers25
- Seqstudio ™ Remote Monitoring App Overview26
- Network Connection Options27
- Network and Password Security Requirements27
  - Network Configuration and Security27
  - Password Security27
- Experiment Types28
- Data Output29
- Secondary Analysis Software29
- Workflow: Connect Cloud-Based Platform or Desktop31
- Workflow: Instrument32
- Precautions for Use33
CHAPTER 2 Prepare the Samples and the Instrument34
- Power on the Instrument34
- Sign in34
- Sign in with the Guest Instrument Profile35
- Sign out35
- Parts of the Home Screen36
- Prepare the Samples37
- Prepare the Instrument39
  - Check the Consumables Status39
  - Load the CBC, the Sample Plate, and the Cartridge41
CHAPTER 3 Use the Instrument with the Connect Cloud-43
- Based Platform43
- Understanding Instrument and Connect Cloud-Based Platform Interaction43
- Connect Cloud-Based Platform Administrators for an Instrument48
- Register and Obtain a Connect Cloud-Based Platform Account50
- Link the Instrument to Your Connect Cloud-Based Platform Account51
- Change Your Own Connect Cloud-Based Platform Instrument Profile PIN52
- Set up Email Notifications from the Instrument53
- And E-Signature (SAE) V2.0 Module55
CHAPTER 4 Use the Instrument with the Security, Auditing56
- Overview of the Security, Auditing, and E-Signature (SAE) V2.0 Module Components56
  - Overview of the Security, Auditing, and E-Signature (SAE) V2.056
  - Module Components56
- Configuring the SAE Module57
- Instrument Functionality When SAE Is Enabled or Disabled58
- Connect the Instrument to an SAE Server (Administrator Only)58
- Enable SAE on the Instrument and Specify the SAE Server (Administrator Only)59
- Disable SAE (Administrator Only)59
  - Enable SAE on the Instrument and Specify the SAE Server59
  - (Administrator Only)59
- Sign in with SAE Enabled60
- Specify Audit Reasons61
- E-Signature Requirements When You Start a Run61
- Sign a Plate Setup63
- View E-Signature Records for a Plate Setup63
- Sign a Dye Calibration or an Install Run64
- View E-Signature Records for a Dye Calibration or an Install Run64
- Signing in after Automatic Screen Locking64
- Use the Instrument When the SAE Server Is Offline65
- Auditing of Imported Plate Setups65
- SAE Error Messages and Actions66
CHAPTER 5 Create or Modify a Plate Setup from the67
- Plate Manager67
- Overview of Plate Setup Settings67
- Set up a Plate Using Default Settings (Plate Manager)69
- Additional Plate Settings (Plate Manager)74
CHAPTER 6 Create or Modify a Plate Setup from the Instrument77
- PSM and CSV Plate Setup Files for Import into the Instrument78
- Shared (Public), Hidden (My Plates), and Guest Plate Setup Files79
- Overview of Plate Setup Settings79
- (Optional) Set up for Auto Export of Sample Data Files (AB1 and FSA)80
- Set up a Plate Using Default Settings (Instrument)81
- Set Optional Plate Settings (Instrument)87
- Load the Plate or the Tube Assembly92
CHAPTER 7 Start and Monitor a Run93
- Select a Plate Setup and Start a Run93
  - Automatic File Cleanup94
- Lock the Touchscreen95
- Monitor a Run from the Connect Cloud-Based Platform95
- Monitor a Run from a Mobile Device103
- Monitor a Run from the Instrument105
- Unload the Plate or the Tube Assembly109
CHAPTER 8 View and Analyze Results110
- View Results in the Remote Monitoring App on the Connect Cloud-Based Platform110
- View Results on the Instrument111
- Export Results from the Instrument (Sample Data Files and QC Reports)121
- Analyze Data121
CHAPTER 9 Manage the Software (Plate Manager)122
- Add a Custom Dye Calibration to the Plate Manager122
- Download a Plate Setup Template as a CSV File122
- Save a Plate Setup as a PDF123
- Save a Plate Setup as a CSV File123
- Create a Plate Setup Template123
- Delete Plate Setups124
- Manage Email Notifications in the Connect Cloud-Based Platform124
- Manage Run Modules125
- Manage Size Standards125
- Manage Analysis Settings126
  - Fragment/Hid Analysis Settings (Size Calling)126
  - Sequencing Settings (Base Calling)129
CHAPTER 10 Manage the Software (Instrument)130
- Connect the Instrument to a Network Drive130
- Link the Instrument to Your Connect Cloud-Based Platform Account136
- Lock the Touchscreen137
- Manage Plate Setups138
  - Export or Delete a Plate Setup (PSM File)138
  - Import a Plate Setup from a CSV or PSM File139
- Manage Run Settings (Instrument)139
- Manage Instrument Settings147
- Manage Instrument Profiles on the Instrument151
- Manage Storage Space153
CHAPTER 11 Maintain the Instrument156
- Regular Maintenance Tasks156
- Manage the Cartridge158
- Install Cathode Buffer166
- Troubleshooting Resources169
APPENDIX A Troubleshooting170
- Troubleshooting Workflow170
- Export Log Files for Plates, Install Runs, Injections, and Instrument170
- View the Raw Data and the EPT Plot171
- Data Quality Alerts171
- Sizecalling and Basecalling Quality Alerts171
- Check Size Standard Quality172
- Instrument Troubleshooting173
- Cartridge Troubleshooting174
- Sample and Data Troubleshooting175
- EPT Data180
- Software Troubleshooting181
- Service Tools183
APPENDIX B Link the Instrument to Your Connect Cloud- Based Platform Account-Detailed Instructions184
- Workflow: Set up the Instrument for Connect Cloud-Based Platform Access184
- Network Requirements184
- Link the Instrument from a Mobile Device185
  - The Instrument186
  - Register the Instrument with the Instrument Connect App186
- Link the Instrument Using a Link Code186
- Set up Email Notifications from the Instrument190
APPENDIX C Dye Calibration and Install Standard Checks192
- Calibrate Dyes192
- Perform an Install Run203
APPENDIX D Create and Run an HID Plate212
- HID Analysis Requirements212
- Pull-Up Reduction Feature213
- Resolution Algorithm214
- Workflow: HID Analysis215
- HID Install Run215
- HID Run Module, Dye Sets, Size Standard Definitions, and Kits216
- Manage Kits (HID Applications Only)217
APPENDIX E Run Modules218
- Run Modules, Read Lengths, Size Ranges, and Run Times218
APPENDIX F Parts and Materials220
- Required Materials Not Supplied220
APPENDIX G Instrument Specifications and Layout222
- Instrument Dimensions222
- Instrument Clearances222
- Environmental Requirements223
- Electrical Requirements224
- Electrical Protective Devices224
- Network Requirements225
- Safety Requirements225
  - Safety Practices225
  - Required Safety Equipment226
APPENDIX H Safety227
- Symbols on this Instrument227
  - Conformity Symbols228
- Safety Alerts on this Instrument229
- Safety Information for Instruments Not Manufactured by Thermo Fisher Scientific230
- Instrument Safety230
- Safety and Electromagnetic Compatibility (EMC) Standards232
- Chemical Safety234
- Biological Hazard Safety235
- Documentation and Support236
- Related Documentation236
- Customer and Technical Support236
- Limited Product Warranty237
- Index238

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