Thermo Scientific appliedbiosystems SeqStudio Flex Series User manual

For Research Use Only. Not for use in diagnostic procedures.
SeqStudio™Flex Series Genetic Analyzer with
Instrument Software v1.0
USER GUIDE
Catalog Numbers A50369
Publication Number 100104689
Revision A

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
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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. 100104689
Revision Date Description
A 26 January 2022 New document for SeqStudio™Flex Series Genetic Analyzer with
Instrument Software v1.0.
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.
NOTICE TO PURCHASER: DISCLAIMER OF LICENSE: Purchase of this software product alone does not imply any license under any
process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by
Thermo Fisher Scientific, either expressly, or by estoppel.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2022 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ................................................ 16
Product description ............................................................ 16
Precautions for use ........................................................ 17
Instrument components .................................................... 18
Instrument interior components ............................................. 21
Power and communication connections ...................................... 22
Theory of operation ............................................................ 23
Preparing samples ......................................................... 23
Preparing the instrument .................................................... 23
During a run ............................................................... 24
Results ................................................................... 24
Materials for routine operation ................................................... 24
Instrument consumables handling, usage limits, and expiration ...................... 25
Configuring the instrument to prevent the use of consumables beyond
expiration and usage limits ................................................ 25
Important notice regarding use of consumables that exceed supported limits ..... 25
Buer storage, usage, and limits ............................................. 26
Polymer storage, usage, and limits ........................................... 26
Conditioning reagent storage, usage, and limits ............................... 27
Capillary array storage and usage ........................................... 27
Hi‑Di™Formamide storage and usage ........................................ 28
About the SeqStudio™Flex Series Instrument Software v1.0 ......................... 28
Profile and sign in options .................................................. 29
Parts of the software ....................................................... 35
Companion software ....................................................... 49
Secondary analysis software ................................................ 50
Network connection options ..................................................... 51
Network and password security requirements ..................................... 52
Network configuration and security .......................................... 52
Password security ......................................................... 52
SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 3

■CHAPTER 2 Get started .......................................................... 53
Sign in ........................................................................ 53
Profile and sign in options ....................................................... 55
Create a local profile (one time only) .......................................... 55
Sign in ................................................................... 57
Switch user or sign out .................................................... 59
Sign in (if another user is signed in) .......................................... 60
Workflow: Create a plate, start and monitor a run, then view results .................. 62
Prepare the instrument .......................................................... 64
Review upcoming maintenance .............................................. 64
Check consumables status ................................................ 66
Check instrument status ................................................... 67
Preheat the instrument oven and the detection cell ............................. 68
Check for leaks and spills ................................................... 68
Check buer fill levels ...................................................... 70
Replenish consumables .................................................... 71
Ensure proper installation of CBC septa ...................................... 71
Control the LED light, speaker volume, and screen brightness ................... 72
■CHAPTER 3 Prepare the samples ................................................ 73
Sample preparation guidelines ................................................... 73
Plate and strip-tube layout ...................................................... 75
Prepare and assemble sample plates ............................................. 76
Prepare sample plates ...................................................... 76
Prepare the plate assembly ................................................. 77
■CHAPTER 4 Create a plate file on the instrument ............................. 83
Create, copy, or import a plate file ............................................... 83
Options for creating plate files ............................................... 83
Create a plate file .......................................................... 84
Copy a plate file ........................................................... 85
Import a plate file .......................................................... 86
Enter plate properties ........................................................... 88
Enter injection properties ........................................................ 89
Specify replicate injections ...................................................... 92
Enter sample names, sample types, and custom fields .............................. 93
Contents
4SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

■CHAPTER 5 Create a plate file in the Plate Manager software ................ 95
Options for creating plate files in the Plate Manager software ....................... 95
Get started with the Plate Manager software (desktop) ............................. 96
About the SeqStudio™Plate Manager 2.0 software (desktop) .................... 96
Access the Plate Manager software (desktop) ................................. 99
Parts of the Plate Manager software (desktop) home screen ................... 101
Connect the Plate Manager software (desktop) to an instrument ............... 103
Get started with the Plate Manager software (cloud) ............................... 105
About the SeqStudio™Plate Manager 2.0 Software (Thermo Fisher™Connect) ... 105
Access the Plate Manager software (cloud) .................................. 111
Parts of Plate Manager software (cloud) home screen ......................... 112
Connect Plate Manager software (cloud) to an instrument .................... 114
Set up a plate file ............................................................. 115
Create or open a plate file (PSM file) ........................................ 115
Enter plate properties ..................................................... 116
Enter sample and injection information ...................................... 116
Save a plate file .......................................................... 119
Keyboard shortcuts and examples .............................................. 121
Set up cloud analysis in the Plate Manager software (cloud) ....................... 124
Print the plate layout .......................................................... 125
Send a plate file to the Inbox on the instrument ................................... 126
Additional functions in the Plate Manager software ................................ 127
Load or download an example plate file ..................................... 127
Specify replicate injections (Add run module function) ........................ 128
Use the list view in the Plate tab ............................................ 128
Define custom fields ...................................................... 129
Save a plate file in CSV format ............................................. 129
Export or download a plate file in PSM format ................................ 129
Manage the software ...................................................... 131
■CHAPTER 6 Start and monitor a run .......................................... 136
Load and unload a plate ....................................................... 136
Load a plate into the instrument ............................................ 136
Unload a plate from the instrument ......................................... 139
Link a plate file and start a run .................................................. 140
Unlink a plate file ............................................................. 144
Processes that the instrument performs during a run .............................. 144
Pre-run check messages and plate alerts during a run ............................. 146
Pre-run checks when a plate run starts or a re-injection or a cancelled
injection is added to the Run queue ....................................... 146
Pre-run checks before each injection or when a paused run is resumed ......... 146
Contents
SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 5

Run plates with the automated barcode workflow ................................. 147
Create the plate files before the barcoded plates are loaded into the drawer ..... 147
Pre-run checks and plate alerts in an automated barcode run .................. 149
View alert and notification details ............................................... 149
Auto-spectral calibration during an injection ...................................... 150
Auto-spectral calibration overview .......................................... 150
Auto-spectral calibration requirements ...................................... 151
Auto-spectral calibration results ............................................ 152
View real-time results in the home screen ........................................ 153
Pause the instrument in the home screen ........................................ 157
Use the Run queue to monitor a run on the instrument ............................ 160
Parts of the Run Queue screen ............................................. 160
View real-time results in the Run Queue screen .............................. 162
Change the injection list order .............................................. 163
Cancel or add injections or specify re-injections in the Run Queue screen ....... 165
Pause the instrument in the Run Queue screen ............................... 166
■CHAPTER 7 View results on the instrument ................................... 169
Options for viewing results on the instrument ..................................... 169
View results for a completed run (Run history).................................... 170
Export results from the instrument—Results and data files, logs, and reports ......... 171
Sample QC and quality alerts .................................................. 172
Use the electropherogram screen ............................................... 173
Sequence analysis results ...................................................... 175
Parts of the sequencing electropherogram screen ............................ 175
Sequencing results and well details ......................................... 176
Understanding Quality Values (QVs) ......................................... 178
Fragment analysis results ...................................................... 179
Parts of the fragment analysis electropherogram screen ....................... 179
Fragment analysis results and well details ................................... 180
■CHAPTER 8 Use the Remote Monitoring software to monitor runs,
view results, and use cloud analysis ........................................... 182
Monitor a run from the Remote Monitoring software ............................... 182
Open the Remote Monitoring software from the Plate Manager software (cloud) . 182
Open the Remote Monitoring software from the InstrumentConnect software .... 183
Parts of the Remote Monitoring software home screen ........................ 184
Plate file requirements for viewing analyzed and cloud results .................. 187
View instrument notifications in your Thermo Fisher™Connect account .......... 188
Set up email notifications from the instrument ................................ 189
View real-time results in the Remote Monitoring software ...................... 190
Sequencing results ....................................................... 192
Fragment analysis results .................................................. 192
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6SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Cancel injections or specify re-injections in the Remote Monitoring software .... 192
Pause the instrument from the Remote Monitoring screen, resume from the
instrument home screen ................................................. 193
Monitor a run from a mobile device .............................................. 193
Register the instrument with the InstrumentConnect app ...................... 193
Monitor a run from a mobile device ......................................... 195
View results in the Remote Monitoring software ................................... 198
View results for a completed run in the Remote Monitoring software (Run
History tab) ............................................................ 198
Export a results report from the Remote Monitoring software ................... 201
Download results from the Remote Monitoring software ....................... 201
Viewing spectral calibration or install run results in the Remote
Monitoring software ..................................................... 202
Use cloud analysis in the Remote Monitoring software ............................. 202
Automated cloud analysis with secondary analysis software ................... 202
Workflow: cloud analysis .................................................. 203
Set up cloud analysis for a completed run in the Remote Monitoring software .... 205
Access cloud analysis results from the Remote Monitoring software ............ 207
■CHAPTER 9 Use the instrument with Thermo Fisher™Connect ............. 210
Overview of Thermo Fisher™Connect features .................................... 211
Administrator set up for Thermo Fisher™Connect ................................. 211
User set up for Thermo Fisher™Connect ......................................... 212
Local profile and cloud profile: when to use, user name, and user initials ............. 213
Sign in to apps.thermofisher.com and access the InstrumentConnect software ..... 215
(Recommended) Link directly to your Thermofisher.com account ................... 217
Link a local profile to your Thermofisher.com account (one time) .................... 220
Sign in to the instrument with a cloud profile ..................................... 222
Re-link the instrument to your cloud profile ....................................... 223
Disconnect the instrument from your cloud profile ................................. 224
Change your cloud profile PIN ................................................. 225
Set up email notifications from the instrument .................................... 226
Tasks for the cloud administrator of an instrument ................................ 228
Enable or disable Thermo Fisher™Connect access on the instrument
(administrator only) ..................................................... 228
Thermo Fisher™Connect cloud administrator functions ........................ 229
Manage the users and administrators of your instrument ...................... 229
Change the instrument name in the InstrumentConnect software (cloud
administrator only) ...................................................... 230
For more information on using Thermo Fisher™Connect ........................... 231
Use voice commands ......................................................... 231
Enable (register) the voice command function ................................ 231
Disable the voice command function ........................................ 232
Use voice commands ..................................................... 232
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SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 7

Basic voice commands .................................................... 234
Interactive voice command—start run ....................................... 234
Microphone icon indicators for voice commands .......................... 235
■CHAPTER 10 Use the instrument with the Security, Auditing, and
E‑signature (SAE) v2.1 module ................................................. 237
Overview of the Security, Auditing, and E‑signature (SAE) v2.1 module components ... 238
Configuring the SAE module and setting permissions .............................. 239
Functions that are not available when the SAE module is enabled ................... 240
Enable SAE mode on the instrument and specify the SAE server (administrator only) .. 240
Disable SAE mode on the instrument (administrator only) .......................... 243
Sign in to the instrument with SAE enabled ....................................... 244
Audit reason requirements ..................................................... 245
E-signature requirements for starting a spectral, install, or regular run ............... 245
Signing an object before a regular run is started .................................. 246
Signing an object when a regular run is started ................................... 247
Signing during an automated barcode run ........................................ 249
Displaying signatures .......................................................... 249
Use the instrument when the SAE server is oine ................................. 250
SAE error messages and actions ................................................ 251
■CHAPTER 11 Manage library resources on the instrument ................. 252
Overview of libraries ........................................................... 253
General library procedures ..................................................... 255
Create a new entry from a factory-provided or locked entry .................... 255
Lock or unlock a library entry ............................................... 255
Copy a library entry ....................................................... 255
Edit a library entry ........................................................ 256
Import a library entry ...................................................... 256
Export a library entry ...................................................... 256
Filter library lists .......................................................... 257
Delete a library entry ...................................................... 258
Plate files library ............................................................. 258
Plate file definition ........................................................ 258
Create a plate file ......................................................... 259
Define custom fields ...................................................... 262
Export or delete a plate file ................................................ 264
Import a plate setup from a CSV or PSM file ................................. 264
Plate file Properties tab ................................................... 265
Plate file Plate tab ........................................................ 267
Plate file Edit Injection Properties screen .................................... 268
Plate file Edit Well Properties screen (sample name entry) ..................... 271
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8SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Run modules library ........................................................... 272
Run module overview ..................................................... 272
Run module provided ..................................................... 272
Create a new run module ................................................. 272
Run module settings ...................................................... 273
Size standards library ......................................................... 275
Size standard overview .................................................... 275
Size standard definition files provided ....................................... 275
Create a new size standard ................................................ 276
Modify a factory-provided normalization size standard ........................ 277
Size standard normalization feature ......................................... 278
File Name Conventions library ................................................. 278
File name convention overview ............................................. 278
Create a new file name convention .......................................... 279
File name convention settings .............................................. 282
Injection protocols library ...................................................... 283
Injection protocol overview ................................................ 283
Create a new injection protocol ............................................ 283
Injection protocol settings ................................................. 284
Dye sets library .............................................................. 285
Dye set overview ......................................................... 285
Create a new dye set ...................................................... 285
Create a custom dye set ................................................... 286
Dye set settings .......................................................... 286
Analysis settings library ....................................................... 288
Analysis settings overview ................................................. 288
Create a new analysis settings ............................................ 289
Analysis settings—Sequencing ............................................. 291
Analysis settings—Fragment analysis ....................................... 295
Results Groups library ........................................................ 301
Results group overview .................................................... 301
Create a new results group ................................................ 302
■CHAPTER 12 Run calibrations and install checks ............................ 304
Run a spatial calibration ....................................................... 304
Spatial calibration overview ................................................ 304
When to perform a spatial calibration ........................................ 304
Perform a spatial calibration ............................................... 305
Evaluate the spatial calibration results ....................................... 306
Contents
SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide 9

Example spatial profiles ................................................... 308
Export spatial calibration results or report .................................... 309
Run a spectral calibration ...................................................... 310
Overview of spectral calibration ............................................ 310
When to perform a spectral calibration ...................................... 311
System dye sets versus custom dye sets .................................... 312
Using BigDye™Direct Cycle Sequencing Kit chemistry ........................ 312
Estimated spectral calibration run times ..................................... 313
Prepare for custom dye set spectral calibration .............................. 314
Prepare for spectral calibration ............................................. 314
Perform a spectral calibration .............................................. 316
View spectral calibration results ............................................ 317
Example spectral calibration data ........................................... 324
Export spectral calibration logs or report .................................... 325
View and export the spectral calibration history .............................. 326
Perform an install run .......................................................... 328
Overview of install run ..................................................... 329
When to perform an install run ............................................. 329
Estimated install run times ................................................. 330
Prepare for the install run .................................................. 330
Perform an install run ..................................................... 333
View sequencing install run results .......................................... 334
View fragment analysis install run results .................................... 347
View, export, or delete an install run history ................................. 352
■CHAPTER 13 Maintain the Instrument ......................................... 354
Maintenance schedule ......................................................... 354
Review upcoming maintenance ............................................ 355
Daily instrument maintenance tasks ......................................... 356
Monthly instrument maintenance tasks ...................................... 357
Annual planned maintenance tasks ......................................... 358
As-needed instrument maintenance tasks ................................... 358
Maintenance wizard overview .................................................. 359
Clean the instrument .......................................................... 361
Export consumables log files ................................................... 363
Install buers (wizard) ......................................................... 363
Install the anode buer container (ABC) ..................................... 364
Install the cathode buer container (CBC) ................................... 367
Replenish, change, flush, and store polymer (wizards) ............................. 370
Precautions for use ....................................................... 370
Replenish polymer or change polymer type (wizard) ........................... 370
Store partially used polymer ............................................... 371
Contents
10 SeqStudio™Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide