Thermo Scientific Applied Biosystems SeqStudio Genetic... User manual

For Research Use Only. Not for use in diagnostic procedures.
SeqStudio™Genetic Analyzer Instrument and
Software
USER GUIDE
for use with:
SeqStudio™Data Collection Software v1.2
SeqStudio™Plate Manager
SeqStudio™Remote Monitoring App
SAE Administrator Console v2.0
SeqStudio™Genetic Analyzer Cartridge (Cat. No. A33671)
SeqStudio™Genetic Analyzer Cartridge v2 (Cat. No. A41331)
Publication Number MAN0018646
Revision A.0

Manufacturer:
Life Technologies Holdings Pte Ltd |
Block 33 |
Marsiling Industrial Estate Road 3 |
#07-06, Singapore 739256
Products:
SeqStudio™Genetic Analyzer
SeqStudio™Data Collection Software
SeqStudio™Plate Manager (desktop)
SeqStudio™Genetic Analyzer Cartridge
SeqStudio™Genetic Analyzer Cartridge v2
Security, Auditing, and E‑signature (SAE) v2.0 module
Manufacturer: Life Technologies
Corporation | 200 Oyster Point Blvd |
South San Francisco, CA 94080 |
USA
Products:
SeqStudio™Remote Monitoring App
Manufacturer: Life Technologies
Corporation | 35 Wiggins Avenue |
Bedford, MA 01730
Products:
SeqStudio™Genetic Analyzer Cathode Buffer Container
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0018646
Revision Date Description
A.0 4 November 2019 New user guide for SeqStudio™Data Collection Software v1.2. The v1.2
software includes options for HID kits. This user guide replaces
Pub. No. MAN0016138.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ...................................... 12
Instrument overview ........................................................... 13
Parts of the instrument ......................................................... 14
Instrument status indicator ................................................. 15
SeqStudio™Genetic Analyzer consumables ........................................ 15
Cartridge ................................................................. 16
SeqStudio™Genetic Analyzer Cathode Buffer Container ........................ 20
Radio frequency identification ............................................... 20
Important notice regarding use of consumables that exceed supported limits ..... 21
Software features .............................................................. 22
SeqStudio™Plate Manager overview .............................................. 24
Computer and operating system options ...................................... 25
Recommended browsers ................................................... 25
SeqStudio™Remote Monitoring App overview ...................................... 26
Network connection options ..................................................... 27
Network and password security requirements ..................................... 27
Network configuration and security .......................................... 27
Password security ......................................................... 27
Experiment types .............................................................. 28
Data output .................................................................... 29
Secondary analysis software .................................................... 29
Workflow: Connect cloud-based platform or desktop ............................... 31
Workflow: instrument .......................................................... 32
■CHAPTER 2 Prepare the samples and the instrument .............. 33
Precautions for use ............................................................ 33
Power on the instrument ....................................................... 34
Sign in ........................................................................ 34
Sign in with the Guest instrument profile .......................................... 35
Sign out ....................................................................... 35
Parts of the home screen ....................................................... 36
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Prepare the samples ........................................................... 37
Sample preparation guidelines .............................................. 37
Plate layout and loading guidelines .......................................... 38
Prepare the plate .......................................................... 38
Prepare the tubes .......................................................... 39
Prepare the instrument ......................................................... 39
Check the consumables status .............................................. 39
Load the CBC, the sample plate, and the cartridge ............................. 41
■CHAPTER 3 Use the instrument with the Connect cloud-
based platform ........................................................... 43
Understanding instrument and Connect cloud-based platform interaction ............. 43
"Connect" versus "link" .................................................... 43
First user who links is assigned administrator role ............................ 43
Local versus Connect cloud-based platform instrument profiles ................. 44
If you link when you
are signed in to the instrument ............................ 44
If you link when you are not signed in to the instrument ......................... 45
Connect cloud-based platform instrument profile roles and functions ............ 47
For more information on using the Connect cloud-based platform ............... 47
Connect cloud-based platform administrators for an instrument ..................... 48
Connect cloud-based platform administrator functions ......................... 48
Assign instrument administrator role to other users ........................... 48
Manage the users and administrators of your instrument ....................... 49
Disconnect individual users from an instrument ............................... 50
Register and obtain a Connect cloud-based platform account ........................ 50
Link the instrument to your Connect cloud-based platform account .................. 51
Change your own Connect cloud-based platform instrument profile PIN .............. 52
Set up email notifications from the instrument ..................................... 53
■CHAPTER 4 Use the instrument with the Security, Auditing,
and E‑signature (SAE) v2.0 module .................................... 55
Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ..... 56
Configuring the SAE module ..................................................... 57
Instrument functionality when SAE is enabled or disabled ........................... 58
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
Sign in with SAE enabled ........................................................ 60
Specify audit reasons ........................................................... 61
E-signature requirements when you start a run .................................... 61
Sign a plate setup .............................................................. 63
View E-signature records for a plate setup ........................................ 63
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Sign a dye calibration or an install run ............................................ 64
View E-signature records for a dye calibration or an install run ...................... 64
Signing in after automatic screen locking ......................................... 64
Use the instrument when the SAE server is offline ................................. 65
Auditing of imported plate setups ................................................ 65
SAE error messages and actions ................................................. 66
■CHAPTER 5 Create or modify a plate setup from the
Plate Manager ............................................................ 67
Overview of plate setup settings ................................................. 67
Set up a plate using default settings (Plate Manager) ............................... 69
Access the Plate Manager on the Connect cloud-based platform ................. 69
Access the Plate Manager on the desktop ..................................... 69
Create or open a plate setup PSM file ........................................ 69
Enter plate properties ...................................................... 70
Assign wells: Sample and run information .................................... 71
Keyboard shortcuts for the sample table ...................................... 72
Save a plate setup in the Plate Manager ...................................... 73
Additional plate settings (Plate Manager) ......................................... 74
Specify replicate injections ................................................. 74
Edit analysis settings ....................................................... 75
Modify the default file name convention ....................................... 75
Hide or share a plate (Plate setup security)................................... 76
Define custom fields ....................................................... 76
■CHAPTER 6 Create or modify a plate setup from the instrument .. 77
PSM and CSV plate setup files for import into the instrument ........................ 78
Shared (public), hidden (my plates), and guest plate setup files ...................... 79
Overview of plate setup settings ................................................. 79
(Optional) Set up for auto export of sample data files (AB1 and FSA) .................. 80
Set up a plate using default settings (instrument) .................................. 81
Create or import a plate setup ............................................... 81
Enter plate properties ...................................................... 82
Assign wells: run module, size standard, dye set, and kit ....................... 84
Assign wells: sample name, sample type, and custom fields .................... 86
Set optional plate settings (instrument) ........................................... 87
Specify replicate injections .................................................. 87
Modify analysis settings .................................................... 87
Modify the default file name convention ....................................... 88
Hide or share a plate (Plate setup security)................................... 89
Define custom fields ....................................................... 89
(Optional) View the injection list, change injection settings or order, or
specify replicates and re-injections .......................................... 91
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■CHAPTER 7 Start and monitor a run .................................. 92
Load the plate or the tube assembly .............................................. 92
Select a plate setup and start a run ............................................... 93
Automatic file cleanup ...................................................... 94
Lock the touchscreen ........................................................... 95
Monitor a run from the Connect cloud-based platform .............................. 95
Open the Remote Monitoring App from Instrument Connect App ................ 95
Open the Remote Monitoring App from the Plate Manager ...................... 97
View notifications from the instrument on your Connect cloud-based
platform account .......................................................... 99
View results in the Remote Monitoring App on the Connect cloud-based platform .. 99
Monitor a run from a mobile device .............................................. 103
Monitor a run from the instrument .............................................. 105
(Optional) View the injection list, change injection settings or order, or
specify replicates and re-injections ......................................... 105
View the run status ....................................................... 105
View real-time results ..................................................... 106
Pause a plate or cancel or stop injections .................................... 106
View results when the run is completed ..................................... 107
Unload the plate or the tube assembly ........................................... 109
■CHAPTER 8 View and analyze results ............................... 110
View results in the Remote Monitoring App on the Connect cloud-based platform ..... 110
View results on the instrument ................................................. 111
View results when the run is completed ..................................... 111
Fragment/HID analysis results ............................................. 113
Sequence analysis results ................................................. 115
EPT plot ................................................................. 117
View results for a previously run plate (run history) ........................... 118
Data quality alerts ........................................................ 119
Sizecalling and basecalling quality alerts ................................... 119
Edit injection parameters and re-inject samples .............................. 120
Export a report (QC report) ................................................. 120
Export results from the instrument (sample data files and QC reports) ............... 121
Analyze data .................................................................. 121
■CHAPTER 9 Manage the software (Plate Manager) ................ 122
Add a custom dye calibration to the Plate Manager ............................... 122
Download a plate setup template as a CSV file .................................... 122
Save a plate setup as a PDF .................................................... 123
Save a plate setup as a CSV file ................................................. 123
Create a plate setup template .................................................. 123
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Delete plate setups ............................................................ 124
Manage email notifications in the Connect cloud-based platform .................... 124
Manage run modules .......................................................... 125
Manage size standards ........................................................ 125
Manage analysis settings ...................................................... 126
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 drive ....................................... 130
Determine IP address for a computer on a network ........................... 130
Create folders and enable network folder sharing ............................ 131
Connect to a network drive ................................................. 132
Set up a default Connect cloud-based platform location for opening plate setups . 132
Set up a default Connect cloud-based platform location for saving results
(auto export) ............................................................. 133
Set up a default network location for opening plate setups ..................... 133
Set up a default network location for saving results (auto export) ............... 134
Link the instrument to your Connect cloud-based platform account ................. 136
Lock the touchscreen .......................................................... 137
Manage plate setups .......................................................... 138
Export or delete a plate setup (PSM file) ..................................... 138
Import a plate setup from a CSV or PSM file .................................. 139
Manage run settings (instrument) ............................................... 139
Manage run modules ...................................................... 139
Manage size standard definitions ........................................... 142
Manage analysis settings .................................................. 142
Modify the default file name convention ..................................... 146
Manage instrument settings .................................................... 147
Display instrument hardware and software information ....................... 147
Change the instrument name .............................................. 148
Enable Demo mode ....................................................... 148
Manage date and time settings ............................................. 148
Manage the network configuration .......................................... 149
Check for software updates (administrator only) .............................. 150
Manage instrument profiles on the instrument .................................... 151
Local instrument profile roles and functions ................................. 151
Create a local instrument profile for another user (administrator only) .......... 151
Change the role of a local instrument profile (administrator only) ............... 152
Delete an instrument profile from an instrument (administrator only) ........... 152
Delete the PIN for a local instrument profile (administrator only) ............... 152
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Create your own local instrument profile .................................... 153
Change your own local instrument profile PIN ................................ 153
Manage storage space ......................................................... 153
Automatic file cleanup ..................................................... 153
Export or delete a plate setup (PSM file) ..................................... 154
Export results from the instrument (sample data files and QC reports) .......... 154
Delete a run history ....................................................... 155
Back up user data (plates and results) (administrator only) .................... 155
■CHAPTER 11 Maintain the instrument .............................. 156
Regular maintenance tasks .................................................... 156
Check the cathode buffer fill level .......................................... 156
Clean the instrument exterior and touchscreen ............................... 157
Clean the autosampler .................................................... 157
Manage the cartridge .......................................................... 158
Cartridge storage ......................................................... 158
Set cartridge storage mode (administrator only) .............................. 159
Check or export the Instrument-cartridge history ............................ 160
Check or export the cartridge history ....................................... 160
Fill the capillary array and refresh the polymer delivery system ................ 161
Remove the cartridge ..................................................... 161
Insert the cartridge ....................................................... 161
Store the cartridge ........................................................ 163
SeqStudio™Integrated Capillary Protector ................................... 164
Long-term on-instrument cartridge storage ................................. 165
Install cathode buffer .......................................................... 166
SeqStudio™Genetic Analyzer Cathode Buffer Container storage ................ 166
Remove the SeqStudio™Genetic Analyzer Cathode Buffer Container ............ 166
Assemble the SeqStudio™Genetic Analyzer Cathode Buffer Container (CBC) ..... 166
Insert the Cathode Buffer Container ........................................ 167
■APPENDIX A Troubleshooting ........................................ 169
Troubleshooting resources ..................................................... 169
Troubleshooting workflow ...................................................... 170
Export log files for plates, install runs, injections, and instrument ................... 170
View the raw data and the EPT plot .............................................. 171
Data quality alerts ............................................................ 171
Sizecalling and basecalling quality alerts ........................................ 171
Check size standard quality .................................................... 172
Instrument troubleshooting .................................................... 173
Cartridge troubleshooting ...................................................... 174
Sample and data troubleshooting ............................................... 175
EPT data .................................................................... 180
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Software troubleshooting ...................................................... 181
Service tools ................................................................. 183
■APPENDIX B Link the instrument to your Connect cloud-
based platform account—detailed instructions ...................... 184
Workflow: Set up the instrument for Connect cloud-based platform access ........... 184
Network requirements ........................................................ 184
Link the instrument from a mobile device ........................................ 185
Create a Connect cloud-based platform PIN and generate the QR code on
the instrument ........................................................... 185
Register the instrument with the Instrument Connect App ..................... 186
Link the instrument using a link code ............................................ 186
Set up email notifications from the instrument .................................... 190
■APPENDIX C Dye calibration and install standard checks ......... 192
Calibrate dyes ................................................................ 192
Overview of system dye set and custom dye set calibration .................... 192
System versus custom dyes ................................................ 192
Factory, auto, and manual calibration ....................................... 193
Determine if manual calibration is required .................................. 193
Perform a system dye calibration .......................................... 195
Perform a custom dye calibration ........................................... 197
View the dye calibration history ............................................ 201
Import or export a custom dye set .......................................... 202
Perform an install run ......................................................... 203
Overview of install checks ................................................. 203
Perform an install run ..................................................... 204
View install run results .................................................... 205
Export the install run report ............................................... 208
View the install run history ................................................. 210
■APPENDIX D Create and run an HID plate .......................... 212
HID analysis requirements ..................................................... 212
Pull-up reduction feature ...................................................... 213
Resolution algorithm .......................................................... 214
Workflow: HID analysis ........................................................ 215
HID install run ................................................................ 215
HID run module, dye sets, size standard definitions, and kits ....................... 216
Manage kits (HID applications only) ............................................. 217
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■APPENDIX E Run modules ........................................... 218
Run modules, read lengths, size ranges, and run times ............................ 218
■APPENDIX F Parts and materials .................................... 220
Required materials not supplied ................................................ 220
■APPENDIX G Instrument specifications and layout ................ 222
Instrument dimensions ........................................................ 222
Instrument clearances ......................................................... 222
Environmental requirements ................................................... 223
Electrical requirements ........................................................ 224
Electrical protective devices .................................................... 224
Network requirements ........................................................ 225
Safety requirements ........................................................... 225
Safety practices .......................................................... 225
Required safety equipment ................................................ 226
■APPENDIX H Safety ................................................... 227
Symbols on this instrument .................................................... 227
Conformity symbols ....................................................... 228
Safety alerts on this instrument ................................................. 229
Safety information for instruments not manufactured by Thermo Fisher Scientific .... 230
Instrument safety ............................................................. 230
General ................................................................. 230
Physical injury ........................................................... 230
Electrical safety .......................................................... 230
Cleaning and decontamination ............................................. 231
Instrument component and accessory disposal ............................... 231
Laser ................................................................... 231
Safety and electromagnetic compatibility (EMC) standards ......................... 232
Safety compliance ........................................................ 232
EMC .................................................................... 232
Environmental design ..................................................... 233
Radio compliance ......................................................... 233
Chemical safety ............................................................... 234
Biological hazard safety ........................................................ 235
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