ThermoFisher Scientific Applied Biosystems Veriti 4375305 User manual

For Research Use Only. Not for use in diagnostic procedures.
Veriti™Thermal Cycler
USER GUIDE
Catalog Numbers 4375305, 4375786, 4384638, 4388444, 4413751, 4413964, and ZGEXSCVERTI3Y
Publication Number MAN0018441
Revision B.0

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.
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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. MAN0018441
Revision Date Description
B.0 17 June 2021 Addition of information on Fleet Control with InstrumentConnect.
A.0 24 January 2020 Converted into CCMS. Removed sku N801537. Updated figure10.
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TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2021 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 System overview ..................................................... 8
Introducing the Veriti™Thermal Cycler ............................................. 8
About the instrument ........................................................ 8
Using the touchscreen ........................................................... 9
Entering text .............................................................. 10
Entering numerals ......................................................... 11
Menu overview ................................................................ 12
Main Menu screen ......................................................... 12
Settings Menu screen ...................................................... 13
Admin Menu screen ....................................................... 13
Tools Menu screen ........................................................ 14
About run methods ............................................................. 14
What is a run method? ..................................................... 14
Predefined methods ....................................................... 14
Viewing a run method ...................................................... 15
Managing run methods ..................................................... 15
Administrative tasks for run methods ......................................... 16
Copying a run method ...................................................... 17
Printing a run method ...................................................... 17
Deleting a run method ...................................................... 18
Designating a run method as the default ...................................... 18
Creating a shortcut to a run method .......................................... 19
Backing up run methods and other settings ................................... 19
Restoring run methods and other settings .................................... 21
About folders .................................................................. 22
Deleting custom folders .................................................... 22
Renaming custom folders ................................................... 22
■CHAPTER 2 Getting started ...................................................... 24
Installing the Veriti™Thermal Cycler .............................................. 24
Before you start ........................................................... 24
Environmental requirements ................................................. 25
Materials ................................................................. 25
Unpacking the instrument .................................................. 27
Setting up the instrument ................................................... 28
Connecting to a network printer ............................................. 28
Veriti™Thermal Cycler User Guide 3

Connecting multiple instruments ............................................. 29
Powering on .............................................................. 30
Setting up the Veriti™Thermal Cycler ............................................. 30
Recommended instrument settings .......................................... 30
Setting up instrument security and user accounts .............................. 33
Adding users .............................................................. 34
Setting other options ........................................................... 38
Setting idle temperatures for the block(s) and cover ............................ 39
Setting time-outs .......................................................... 39
Configuring main menu shortcuts to functions ................................. 40
About the Thermal Cycler Fleet Control Software ................................... 41
Connect the thermal cycler to the network .................................... 41
■CHAPTER 3 Performing a run .................................................... 42
Selecting disposables .......................................................... 42
Disposables for 96‑well instruments .......................................... 42
Disposables for the 384-well instrument ...................................... 44
Disposables for the 60-well Veriti™Thermal Cycler ............................. 44
Loading samples into the instrument ............................................. 44
Loading Samples in 96-well instruments ...................................... 45
Loading samples in the 384-well instrument ................................... 46
Loading samples in the Veriti™60-well Thermal Cycler .......................... 47
Creating a new run method ...................................................... 47
Editing details ................................................................. 49
Adding a stage ............................................................ 49
Adding a step ............................................................. 50
Editing temperature and time ................................................ 51
Editing ramp rates ......................................................... 52
Creating an AutoDelta step ................................................. 52
Adding a pause ............................................................ 54
Deleting a stage or step .................................................... 55
Creating a VeriFlex™step ................................................... 55
Performing a run ............................................................... 57
Before you begin .......................................................... 57
Monitoring a run ............................................................... 59
Run Monitor screen ........................................................ 59
Actions in the Run Monitor screen during a run ................................ 60
Changing the number of cycles .............................................. 61
Pausing a run ............................................................. 61
Stopping a run ............................................................ 62
Using the Run Monitor button ............................................... 62
If the power fails ........................................................... 63
Viewing and printing the run report ............................................... 63
Removing the samples from the instrument ....................................... 64
Contents
4Veriti™Thermal Cycler User Guide

■CHAPTER 4 Utilities ............................................................... 65
Using GeneAmp™PCR System 9700 run methods ................................. 65
Upgrading system firmware ..................................................... 67
About the upgrade ......................................................... 67
Upgrading the instrument firmware .......................................... 67
Calculating melting temperatures ................................................ 69
Viewing instrument statistics .................................................... 70
Restoring the factory settings .................................................... 70
Running the cycle performance test .............................................. 71
Required materials ......................................................... 72
Procedure ................................................................ 72
Tests using the temperature verification kit ........................................ 72
About the temperature verification kit ......................................... 73
For more information ....................................................... 73
Running the heated cover verification ........................................ 73
Running the temperature verification ......................................... 74
Running the temperature nonuniformity test ................................... 75
TVK recalibration .......................................................... 76
■CHAPTER 5 Maintenance ......................................................... 77
Scheduled maintenance ........................................................ 77
As-Needed maintenance ........................................................ 77
Tests ..................................................................... 77
Cleaning the instrument .................................................... 77
Replacing fuses ........................................................... 80
Parts list ...................................................................... 81
■APPENDIX A Troubleshooting .................................................... 83
■APPENDIX B Returning an instrument for service .............................. 85
■APPENDIX C Disposables ........................................................ 86
Disposables ................................................................... 86
Other supplies for sample handling ............................................... 88
■APPENDIX D Instrument specifications ......................................... 89
System specifications .......................................................... 89
Physical dimensions and electrical specifications .............................. 89
Power and communication connections ...................................... 89
Sample temperature range .................................................. 90
Contents
Veriti™Thermal Cycler User Guide 5

Touchscreen specifications ................................................. 90
Sample well specifications .................................................. 90
Printer specifications ........................................................... 91
■APPENDIX E Predefined run methods ........................................... 92
Predefined run methods ........................................................ 92
AmpliCycle™Seq Run Method .............................................. 93
AmpliTaq Gold™DNA Polymerase Run Method ................................ 93
AmpliTaq Gold™Fast PCR Run Method ....................................... 93
BigDye™Kit Fast Run Method ............................................... 94
BigDye™Kit Standard Run Method ........................................... 94
Fast PCR Run Method ...................................................... 94
General PCR Run Method .................................................. 95
LMS2 Run Method ......................................................... 95
Time Release Run Method .................................................. 95
Touchdown PCR Run Method ............................................... 96
XL PCR Run Method ....................................................... 96
Limited product warranty ........................................................ 96
■APPENDIX F Safety and EMC compliance information ........................ 97
Safety conventions used in this document ........................................ 97
Safety alert words ......................................................... 97
Symbols on instruments ........................................................ 98
Electrical symbols on instruments ........................................... 98
Environmental symbols on instruments ....................................... 98
Safety symbols ............................................................ 99
Safety labels on instruments ................................................ 99
General instrument safety ...................................................... 100
Moving and lifting the instrument ........................................... 100
Operating the instrument .................................................. 100
Cleaning or decontaminating the instrument ................................. 101
Electrical safety ............................................................... 101
Fuses ................................................................... 101
Power ................................................................... 101
Overvoltage rating ........................................................ 101
Safety and electromagnetic compatibility (EMC) standards ......................... 102
Physical hazard safety ......................................................... 102
Moving parts ............................................................. 102
Chemical safety .............................................................. 103
Biological hazard safety ....................................................... 104
Contents
6Veriti™Thermal Cycler User Guide

■APPENDIX G Documentation and support .................................... 105
Customer and technical support ................................................ 105
Limited product warranty ...................................................... 105
Contents
Veriti™Thermal Cycler User Guide 7

System overview
Introducing the Veriti™Thermal Cycler
About the instrument
There are four models of the Veriti™Thermal Cycler:
•Veriti™96-Well Fast Thermal Cycler (PN 4375305), with 0.1–mL sample wells
•Veriti™96-Well Thermal Cycler (PN 4375786), with 0.2–mL sample wells
•Veriti™384-Well Thermal Cycler (PN 4388444), with 0.02–mL sample wells
•Veriti™60-Well Thermal Cycler (PN 4384638), with 0.5–mL sample wells
The Veriti™Thermal Cycler is controlled using a touchscreen display with easy-to-use interface. It is
also compatible with the Applied Biosystems™Thermal Cycler Fleet Control Software. Up to twelve
Veriti™Thermal Cyclers can be connected in a satellite-like format through a network switch. With this
connection, you can transmit run methods from one Veriti™thermal cycler to another and start multiple
thermal cyclers at once.
The Veriti™Thermal Cycler has a run recovery feature. If a power failure occurs during a run, the
instrument will attempt to continue the run when the power returns.
In addition, the Veriti™96-Well Thermal Cyclers have VeriFlex™Blocks™. These are six independently
regulated thermal blocks to aid in designing a primer set and run method for optimal PCR conditions.
Figure 1 The Applied Biosystems™Veriti™thermal cycler
This user guide provides instructions for all four models of the Veriti™Thermal Cycler. Functions which
are not the same for each model are indicated by a comment such as “This function is only available for
the Veriti™96-Well Thermal Cyclers”.
See Appendix D, “Instrument specifications” for detailed specifications of the Veriti™Thermal Cycler.
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8Veriti™Thermal Cycler User Guide

Using the touchscreen
You interact with the instrument using a touchscreen.
Table 1 describes several buttons common to many of the touchscreens.
Table 1 Buttons in the instrument touchscreen
Button Function
Returns to the Main Menu screen.
Returns to the previous screen.
When a run is in progress, displays the Status Report to view any errors that occurred
during the run.
When a run is in progress, displays the Run Monitor screen to view the run.
Scrolls up and down through a list of items.
Displays the run method folders.
Creates a “shortcut” to the selected run method (or methods).
Indicates that a USB drive is connected to the instrument’s USB port.
Opens the Help system.
Chapter 1 System overview
Using the touchscreen 1
Veriti™Thermal Cycler User Guide 9

Entering text
When you touch a field that requires the input of text, the text editor opens (Figure 2).
Figure 2 The instrument text editor
To… Select…
Enter a lowercase letter A letter button.
Enter an uppercase letter
Caps, then the letter(s).
When you are done, select Caps again.
Enter punctuation or other symbols
Symbols then the symbol(s).
When you are done, select Symbols again.
Remove the contents of the entire field
Delete the last letter
Close the editor and save any changes
Chapter 1 System overview
Using the touchscreen
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10 Veriti™Thermal Cycler User Guide

Entering numerals
When you touch a field that requires only numerical input, the numeric editor opens (Figure 3).
Figure 3 The instrument numeric editor
To… Select…
Enter a number A number button.
Delete the last number
Remove the entire contents of the field
Close the editor and save any changes
Chapter 1 System overview
Using the touchscreen 1
Veriti™Thermal Cycler User Guide 11

Menu overview
Main Menu screen
After you log in to the system, the Main Menu screen opens. This screen is the starting point for
operating the instrument. The date, current time, and current user are shown at the bottom of the
screen.
If your system does not require login, the My Account button is not shown.
Figure 4 The Main Menu screen
In the Main Menu screen, select:
•Browse/New Methods to view and work with all the run methods to which you have access (see
“Viewing a run method” on page 15).
•Settings Menu to access various instrument configuration options. If you have administrative
privileges, you access the Admin Menu screen from this screen (see “Settings Menu screen” on
page 13).
•Tools Menu to access instrument tests, tools such as a Tm calculator and run method conversion,
as well as viewing the results of the last run and statistics about the instrument (see “Tools Menu
screen” on page 14).
•My Account to view and edit your account information. If your system does not require login, this
button is not shown.
•The Shortcut buttons allow you to configure instrument functions you frequently use to appear in
the Main Menu screen (see “Configuring main menu shortcuts to functions” on page 40).
•Log O to log o the instrument. You can still log o when a run is in process. If your system does
not require login, the (Power) button is shown instead.
•(Help) to access the Help system.
Chapter 1 System overview
Menu overview
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12 Veriti™Thermal Cycler User Guide

Settings Menu screen
Use this screen to set various instrument configuration options.
For instruments that require login, only Users and Administrators have access to this menu.
Figure 5 The Settings Menu screen, with the Admin Menu button shown
Admin Menu screen
Use this screen to manage user accounts, set instrument security, back up run methods and settings,
upgrade the firmware, and perform other functions.
If your system does not require login, the Manage Users button is not shown.
For instruments that require login, only Administrators have access to this menu.
Figure 6 The Admin Menu screen, available only to users with administrative privileges
Chapter 1 System overview
Menu overview 1
Veriti™Thermal Cycler User Guide 13

Tools Menu screen
Use this screen to access various tools and instrument tests.
Figure 7 The Tools Menu screen, available to all users
For more information about the functions on the Tools Menu, see Chapter 4, “Utilities”
About run methods
What is a run method?
A run method is a set of instructions that specifies how the instrument should heat and cool your
samples. Run methods are stored in the instrument firmware.
Predefined methods
The instrument firmware has 10 pre-defined run methods.
IMPORTANT! The customer is responsible for validation of run methods on the instrument before
use, and for compliance with regulatory requirements that pertain to their procedures and uses of the
instrument.
•AmpliCycle™Seq Run Method
•AmpliTaq Gold™DNA Polymerase Run Method
•AmpliTaq Gold™Fast PCR Run Method
•BigDye™Kit Standard Run Method
•BigDye™Kit Fast Run Method
•Fast PCR Run Method
•General PCR Run Method
•LMS2 Run Method
•Time Release Run Method
Chapter 1 System overview
About run methods
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14 Veriti™Thermal Cycler User Guide

•Touchdown PCR Run Method
•XL PCR Run Method
Each method is stored in the Shared folder. You can edit, copy, and run these predefined methods as
you would any other run method, but you cannot delete them.
For details on these methods, see Appendix E, “Predefined run methods”
Viewing a run method
To view a run method:
1. In the Browse Run Methods screen, select a run method, then select View/Edit.
The run method is displayed:
IMPORTANT! If you are logged on as a Limited User, you can make changes to the run method
but you cannot save it. If you are logged on as a Guest, you can make changes to the run method
but you can only save it to a USB drive.
2. To view:
•Other steps in the run method – Use the arrow buttons at the end of the run method.
•View steps with ramp rates – Select Options4Ramp Rate. The fields showing times update
to show the corresponding ramp rates.
3. When you are done, select to return to the Browse Run Methods screen.
Managing run methods
1. Select Browse/New Methods in the Main Menu screen.
The Browse Last Accessed Run Methods screen displays the most recently accessed run
methods, and lists the total number of run methods in parentheses.
Chapter 1 System overview
About run methods 1
Veriti™Thermal Cycler User Guide 15

2. Select one or more rows to choose a method(s).
3. Select a highlighted row to deselect it.
Administrative tasks for run methods
Table 2 Administrative tasks for run methods
If you want to… Do this…
Sort run methods by dierent criteria Select the title of the column with the criteria by
which you want to sort the run methods.
Select the title a second time to sort in the opposite
order.
View more run methods in the current folder Select (Page Down).
View run methods in a dierent folder Select (folders), then select the folder you want
to view in the Manage Folders All screen.
Start a run Select a run method in the list of run methods, then
select Start Run (see page 57).
Create a new run method Select New (see page 47).
View or edit a run method Select a run method in the list of run methods, then
select View/Edit (see page 49).
Copy one or more run methods Select a run method in the list of run methods, then
select Copy (see page 17).
Print a run method Select a run method in the list of run methods, then
select Print (see page 17).
Delete one or more run methods Select a run method in the list of run methods, then
select Delete (see page 18).
Designate a run method as the default See page 18.
Chapter 1 System overview
About run methods
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16 Veriti™Thermal Cycler User Guide

Table 2 Administrative tasks for run methods (continued)
If you want to… Do this…
Create a shortcut to a run method on the Main Menu Select a run method in the list of run methods, then
select (Create Method Shortcut.)
See page 19.
Back up run methods See page 19.
Restore run methods that you previously backed up See page 21.
Copying a run method
Note: If your instrument requires login, you must have User or Administrator level permissions to copy
a run method.
To copy a run method:
1. Log in as a user with User or Administrator access.
2. In the Browse Run Methods screen, find the run method or methods you want to copy.
3. Select each run method, then select Copy.
4. In the Save Run Method screen:
a. If you are copying one method – select Name, then rename the method and/or select
(Folder) to save the run method to a dierent folder.
or
If you are copying more than one method – select (Folder) to save the run methods to a
dierent folder.
b. As needed, select Reaction Volume, Cover Temperature, and Notes to edit the values. You
can change any of these values when you perform a run with this run method.
c. Select Save & Exit, then OK.
Printing a run method
Note: Before you print a run method, be sure your instrument is connected to a printer. See
“Connecting to a network printer” on page 28.
1. In the Browse Run Methods screen, locate the run method you want to print.
2. Select the run method, then select Print.
Chapter 1 System overview
About run methods 1
Veriti™Thermal Cycler User Guide 17

Deleting a run method
Note: If your instrument requires log in, you must have User or Administrator level permissions to
delete a run method.
To delete a run method:
1. Log in as a user with User or Administrator access.
2. In the Browse Run Methods screen, find the run method you want to delete.
3. Select the run method, then select Delete.
4. In the dialog box that opens, verify the deletion.
5. Select Yes in the message box.
The run method is deleted.
Designating a run method as the default
The run method that is designated as the default method is used as the starting point for all new
methods. The Veriti™Thermal Cycler uses the General PCR run method (shown in “General PCR Run
Method” on page 95) as the default, unless you change to another method.
IMPORTANT! If your instrument requires login, you must have User or Administrator level permissions
to set the default run method. Only a run method in the Shared folder can be set as the default method.
To designate a run method as the default:
1. Log in as a user with User or Administrator access.
2. In the Main Menu screen, select Settings Menu.
3. In the Settings Menu screen, select Set Default Method.
The Set the Default Run Method screen is displayed, with only the run methods in the Shared
folder displayed.
4. Select the run method you wish to designate as the default in the Set the Default Run Method
then select Make Default. Select OK in the message box that opens.
The Settings Menu screen opens and the selected run method is now the default.
Chapter 1 System overview
About run methods
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18 Veriti™Thermal Cycler User Guide

Creating a shortcut to a run method
You can add buttons to the Main Menu screen that allow you to go directly to the Edit Run Method
screen for a particular run method. When login is required, each user can configure his or her own
shortcut buttons; otherwise the shortcut buttons are displayed for all instrument users.
Note: You can also create shortcuts to instrument functions (see “Configuring main menu shortcuts to
functions” on page 40).
1. Select one or more methods in the Browse Run Methods screen, then select (Create Method
Shortcut).
2. In the message box that appears, select OK.
The selected run methods appear as buttons in the Main Menu screen. The name of the method is
followed by the name, in parentheses, of the folder where the method is stored.
Note: Run method names longer than twelve characters will appear truncated on the shortcut
button.
To delete a shortcut to a run method, see “Configuring main menu shortcuts to functions” on page 40.
Backing up run methods and other settings
You can back up the instrument run methods and other settings to a USB drive. All run methods,
folders, user information, and other instrument settings are saved.
Note: If your instrument requires login, you must have Administrator level permissions to back up run
methods and instrument settings.
1. Insert the USB drive into the USB port on the front of the instrument.
2. Log in as a user with Administrator access.
3. In the Main Menu screen, select Settings Menu, then Admin Menu.
Chapter 1 System overview
About run methods 1
Veriti™Thermal Cycler User Guide 19

4. In the Admin Menu screen, select Back Up Methods & Settings.
The Back Up Method and Settings screen is displayed:
5. Select Back Up.
If a back up file already exists, you are prompted to overwrite it.
The instrument copies all run methods, folders, user information, and other instrument settings to
the USB drive, then displays a message box when the backup is complete.
6. Select OK, then select (Close) to return to the Admin Menu screen.
7. Remove the USB drive and store it in a safe place.
Chapter 1 System overview
About run methods
1
20 Veriti™Thermal Cycler User Guide