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Thermo Scientific A50369 Genetic Analyzer Manuals
Manuals and User Guides for Thermo Scientific A50369 Genetic Analyzer. We have
1
Thermo Scientific A50369 Genetic Analyzer manual available for free PDF download: User Manual
Thermo Scientific A50369 User Manual (574 pages)
Genetic Analyzer with Instrument Software v1.0
Brand:
Thermo Scientific
| Category:
Measuring Instruments
| Size: 14.59 MB
Table of Contents
Table of Contents
3
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
25
Expiration and Usage Limits
25
Important Notice Regarding Use of Consumables that Exceed Supported Limits
25
Buffer 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
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 Buffer 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
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
105
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
Load and Unload a Plate
136
Load a Plate into the Instrument
136
CHAPTER 6 Start and Monitor a Run
138
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
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
182
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
Cancel Injections or Specify Re-Injections in the Remote Monitoring Software
192
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
198
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
202
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
Connect
210
CHAPTER 9 Use the Instrument with Thermo Fisher
211
Overview of Thermo Fisher ™ Connect Features
211
Administrator Set up for Thermo Fisher ™ Connect
211
Overview of Thermo Fisher
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
228
(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
230
Administrator Only)
230
For more Information on Using Thermo Fisher ™ Connect
231
Connect
231
Use Voice Commands
231
Enable (Register) the Voice Command Function
231
Disable the Voice Command Function
232
Use Voice Commands
232
Basic Voice Commands
234
Interactive Voice Command-Start Run
234
Microphone Icon
235
CHAPTER 10 Use the Instrument with the Security, Auditing, and E-Signature (SAE) V2.1 Module
238
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 Offline
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
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
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
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 Buffers (Wizard)
363
Install the Anode Buffer Container (ABC)
364
Install the Cathode Buffer 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
Change and Store a Capillary Array (Wizards)
371
Parts of the Capillary Array
372
Install or Change the Capillary Array (Wizards)
374
Store a Capillary Array
375
Maintain the Pump (Wizards)
376
Parts of the Polymer Delivery Pump
376
Avoiding Damage to the Pump Assembly
377
Remove Bubbles from the Polymer Pump (Wizard)
377
Wash the Pump Chamber and Channels (Wizard)
379
Flush the Water Trap (Pump Trap)
379
Shut Down, Move, and Reactivate the Instrument
381
Shutdown the Instrument (Wizard)
381
Move and Level the Instrument
381
Reactivate the Instrument (Wizard)
382
Maintenance Wizard Procedures
382
Change Capillary Array Maintenance Wizard
382
Change Polymer Type (with Change Array Option) Maintenance Wizard
394
Fill Array with Polymer Maintenance Wizard
409
Remove Bubbles Maintenance Wizard
409
Spatial Calibration Maintenance Wizard
412
Replenish Buffers Maintenance Wizard
413
Wash Pump and Channels Maintenance Wizard
415
Replenish Polymer Maintenance Wizard
417
Shut down Instrument Maintenance Wizard
420
Reactivate Instrument Maintenance Wizard
427
CHAPTER 14 Manage the Software (Instrument)
439
Connect the Instrument to a Computer or Network (Hardware Connections)
439
Wired and Wireless Network Options
439
Wired and Wireless Network Connections on the Instrument
440
Antivirus Recommendations for Direct Connection of the Computer to
440
The Instrument
440
Connect the Instrument Directly to a Computer
441
Connect the Software to a Network Drive (Software Settings)
443
Determine the IP Address for a Computer on a Network
443
Create Folders and Enable Network Folder Sharing
444
Connect the Instrument to a Network Drive (Software)
445
Manage Sign-In Profiles
446
Local Profile Roles (Standard and Administrator) and Functions
446
Change the Role of a Local Profile (Administrator Only)
447
Edit Your Own Local Profile
447
Delete a Local Profile or a Cloud Profile from an Instrument (Administrator Only)
447
Create a Local Profile (One Time Only)
448
Change Your Own Local Profile PIN
451
Manage Settings
452
Display Instrument Hardware and Software Information
452
Configure Consumables Usage and Warnings (Administrator Only)
453
Set up Email Notifications from the Instrument
454
(Administrator Only)
455
Enable and Set up Demo Mode
457
Enable/Disable the Internal Barcode Reader (Administrator Only)
459
Set the Power Save Duration (Administrator Only)
459
Connect Access on the Instrument
460
(Administrator Only)
460
Manage Instrument Settings
461
Change the Instrument Name (Administrator Only)
461
Manage Date and Time Settings
462
Update the Software (Administrator Only)
462
Manage the Network Configuration (Administrator Only)
464
Select a Language
465
Configure, Check Status, and Cancel Background Exports and Backups
465
Set the Default Save Location for Results
468
Manage Storage Space
468
Automatic File Cleanup (Autopurge)
468
Export Results from the Instrument-Results and Data Files, Logs, and Reports
469
Delete a Run History
469
Back up User Data (Instrument Settings, Library Items, and Results)
470
(Administrator Only)
470
APPENDIX A Troubleshooting
471
Troubleshooting Workflow
472
Troubleshooting Resources
473
Use Smart Help to Request Assistance from Technical Support or Instrument Service
473
Start a Remote Support Session
475
Inspect the Data-Troubleshooting Procedures
476
View the Raw Data and the EPT Plot
476
Check Size Standard Quality (Fragment Analysis)
476
Monitoring Software
478
Inspect the Instrument -Troubleshooting Procedures
480
View the Instrument Sensor Details and EPT Plot
480
Check the Pump for Bubbles or Debris
480
Additional Troubleshooting Procedures
482
Export Troubleshooting Logs
482
Check the Position of the Cathode Buffer Container (CBC)
483
Use the Manual Commands Function to Move Instrument Components
483
Proximity Sensor
485
Power off or Power on the Instrument
485
Instrument Interior Components
487
QC Error and Alert Troubleshooting
489
QC Errors-Sequencing and Fragment Analysis
489
QC Errors-Sequencing
490
QC Errors-Fragment Analysis
490
QC Errors-Spectral Calibration (Manual)
492
QC Errors-Sequencing or Fragment Analysis Install Run
494
Cloud Analysis Troubleshooting
495
Consumables Troubleshooting
495
Home Screen and General Instrument Software Troubleshooting
496
Install Run Troubleshooting
498
Instrument Troubleshooting
499
Library Troubleshooting
500
Maintenance Wizard Troubleshooting
501
Plate Troubleshooting
501
Plate File Troubleshooting
501
Plate Manager Software Troubleshooting
502
Remote Monitoring Software Troubleshooting
505
RFID Troubleshooting
507
Run Troubleshooting
507
Plate Alert Troubleshooting
507
Plate Alert Troubleshooting (Automated Barcode Workflow)
509
Run History Troubleshooting
511
Run Queue Troubleshooting
511
SAE Troubleshooting
511
Sample and Data Troubleshooting
512
Sequencing and Fragment Applications
513
Sequencing Applications
517
Fragment Analysis Applications
519
Settings Screen Troubleshooting
519
Sign in Troubleshooting
520
Software Troubleshooting
521
Spatial Calibration Troubleshooting
522
Spectral Calibration Troubleshooting
523
Thermo Fisher ™ Connect Troubleshooting
524
Voice Command Troubleshooting
525
APPENDIX B Run Modules and Dye Sets
526
Run Modules, Read Lengths, Size Ranges, and Run Times
526
Dye Sets
530
APPENDIX C Instrument Specifications
531
Instrument Dimensions and Clearance
531
Operating Specifications
533
Environmental Requirements
533
Electrical Requirements
534
Wired and Wireless Network Options and Requirements
535
Network and Firewall Requirements
536
Power and Communication Connections
537
APPENDIX D Catalog Numbers
539
Plates Bases Retainers and Septa
539
Instrument Consumables
540
Sequencing Analysis Reagents and Consumables
540
Fragment Analysis Reagents
541
APPENDIX E Radio Frequency Identification (RFID) Technology
542
RFID Precautions for Use
542
Locations of RFID Read/Write Units
543
RFID Function
543
RFID Specifications
544
RFID Troubleshooting
545
Symbols on this Instrument
546
APPENDIX F Safety
547
Standard Safety Symbols
547
Location of Safety Labels
547
Control and Connection Symbols
549
Conformity Symbols
550
Safety Information for Instruments Not Manufactured by Thermo Fisher Scientific
550
Instrument Safety
550
General
550
Physical Injury
551
Electrical Safety
552
Cleaning and Decontamination
553
Instrument Component and Accessory Disposal
553
Laser Safety
554
Safety and Electromagnetic Compatibility (EMC) Standards
554
Safety Standards
555
EMC Standards
555
Environmental Design Standards
556
Radio Compliance Standards
556
Chemical Safety
558
Biological Hazard Safety
559
APPENDIX G Documentation and Support
560
Related Documentation
560
Customer and Technical Support
561
Limited Product Warranty
561
Index
562
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