Thermo Fisher Scientific Applied Biosystems Veriti™ Thermal Cycler Owner's Manual

Applied Biosystems
Veriti™ Thermal Cycler
User Guide
Applied Biosystems
Veriti™ Thermal Cycler
User Guide
© Copyright 2008, 2010 Applied Biosystems. All rights reserved.
General Laboratory Use.
Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this
document.
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL
APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER
BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.
NOTICE TO PURCHASER:
The Veriti™ Thermal Cycler is covered by US patent claims and corresponding claims in their non-US counterparts. No right is conveyed expressly, by
implication, or by estoppel under any other patent claim, such as claims to apparatus, reagents, kits, or methods such as 5’ nuclease methods. Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City,
California 94404, USA.
TRADEMARKS:
Applera, Applied Biosystems, AB (Design), ABI PRISM, BigDye, and GeneAmp, are registered trademarks and MicroAmp, VeriFlex, and Veriti are
trademarks of Applied Biosystems or its subsidiaries in the U.S. and/or certain other countries.
AmpliCycle, AmpliTaq, and AmpliTaq Gold is a registered trademark of Roche Molecular Systems, Inc.
All other trademarks are the sole property of their respective owners.
Part Number 4375799 Rev. E
06/2010
Contents
Front Matter
Preface
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Safety and EMC Compliance Information
Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . xvii
Chapter 1
System Overview
Introducing the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Using the Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Menu Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
About Run Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
About Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15
Chapter 2
Getting Started
Installing the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Before You Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Environmental Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Unpacking the Veriti™ System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Setting Up the Veriti™ System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Connecting to a Network Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Connecting Together Multiple Instruments . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
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Powering On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
Setting Up the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Recommended Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Setting Up Instrument Security and User Accounts . . . . . . . . . . . . . . . . . . . 2-9
Adding Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Setting Other Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Chapter 3
Performing a Run
Selecting Disposables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Disposables for 96-Well Veriti™ Thermal Cyclers . . . . . . . . . . . . . . . . . . . . . 3-2
Disposables for the 384-Well Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . 3-4
Disposables for the 60-Well Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . 3-4
Loading Samples into the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Loading Samples in Veriti™ 96-Well Thermal Cyclers . . . . . . . . . . . . . . . . . . 3-5
Loading Samples in the Veriti™ 384-Well Thermal Cycler . . . . . . . . . . . . . . . 3-6
Loading Samples in the Veriti™ 60-Well Thermal Cycler . . . . . . . . . . . . . . . . 3-7
Creating a New Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Editing Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
Performing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
Monitoring a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
Viewing and Printing the Run Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
Removing the Samples from the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
Chapter 4
Troubleshooting
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Returning an Instrument for Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Chapter 5
Utilities
Using GeneAmp® PCR System 9700 Run Methods . . . . . . . . . . . . . . . . . . . . . . 5-2
Upgrading System Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Calculating Melting Temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Viewing Instrument Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Restoring the Factory Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Running the Cycle Performance Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Tests Using the Temperature Verification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Running the Heated Cover Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Running the Temperature Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Running the Temperature Nonuniformity Test . . . . . . . . . . . . . . . . . . . . . . 5-13
TVK Recalibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
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Veriti™ Thermal Cycler User Guide
Chapter 6
Maintenance
Scheduled Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
As-Needed Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Replacing Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Appendix A Instrument Specifications
System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Printer Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
Appendix B Disposables
Disposables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2
Other Supplies for Sample Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-4
Appendix C Predefined Run Methods
Predefined Run Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
AmpliCycle® Seq Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
AmpliTaq Gold® DNA Polymerase Run Method . . . . . . . . . . . . . . . . . . . . . . C-3
AmpliTaq Gold® Fast PCR Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-3
BigDye® Kit Fast Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-4
BigDye® Kit Standard Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-4
Fast PCR Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-5
General PCR Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-5
LMS2 Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-6
Time Release Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-6
Touchdown PCR Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-7
XL PCR Run Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-7
Index
Veriti™ Thermal Cycler User Guide
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Veriti™ Thermal Cycler User Guide
Preface
How to Use This Guide
Purpose of This
Guide
The Applied Biosystems Veriti ™ User Guide provides information about installing,
using and maintaining the Applied Biosystems Veriti Thermal Cycler.
Audience
This guide is intended for novice and experienced Veriti Thermal Cycler users who
use the instrument to perform PCR.
Assumptions
Text Conventions
This guide assumes you have knowledge of basic laboratory procedures and PCR
chemistry.
This guide uses the following conventions:
• Bold text indicates user action. For example:
Type 0, then press Enter for each of the remaining fields.
• Italic text indicates new or important words and is also used for emphasis.
For example:
Before analyzing, always prepare fresh matrix.
• A right arrow symbol () separates successive commands you select from a
drop-down or shortcut menu. For example:
Select FileOpenSpot Set.
Right-click the sample row, then select View Filter View All Runs.
User Attention
Words
Two user attention words appear in Applied Biosystems user documentation. Each
word implies a particular level of observation or action as described below:
Note: – Provides information that may be of interest or help but is not critical to the
use of the product.
IMPORTANT! – Provides information that is necessary for proper instrument
operation, accurate chemistry kit use, or safe use of a chemical.
Examples of the user attention words appear below:
Note: The Calibrate function is also available in the Control Console.
IMPORTANT! If your instrument is so configured, you need a valid user ID and
password to log in.
Safety Alert
Words
Safety alert words also appear in user documentation. For more information, see
“Safety Alert Words” on page xii.
Veriti™ Thermal Cycler User Guide
vii
Preface
How to Obtain More Information
Related
Documentation
The following document is shipped with the system:
Applied Biosystems Veriti™ Thermal Cycler Quick Reference Card – Provides a
summary of information about the thermal cycler, its installation, and accessories. It
is designed to help you quickly learn to use the Veriti Thermal Cycler.
A portable document format (PDF) version of this guide is available on the Veriti™
Thermal Cycler Documentation CD.
Note: To open the user documentation on the Veriti™ Thermal Cycler
Documentation CD, use the Adobe® Reader® software available from
www.adobe.com.
Note: For additional documentation, see “How to Obtain Support” on page viii.
Obtaining
Information from
the Help System
Send Us Your
Comments
The Veriti Thermal Cycler has a Help system that describes how to use each feature
of the user interface. Access the Help system by touching
(Help) at the bottom
right corner of the instrument touchscreen.
Applied Biosystems welcomes your comments and suggestions for improving its
user documents. You can e-mail your comments to:
[email protected]
IMPORTANT! The e-mail address above is for submitting comments and suggestions
relating only to documentation. To order documents, download PDF files, or for help
with a technical question, go to http://www.appliedbiosystems.com, then click the
link for Support. (See “How to Obtain Support” below).
How to Obtain Support
Support
Information
For the latest services and support information for all locations, go to
http://www.appliedbiosystems.com, then click the link for Support.
At the Support page, you can:
• Search through frequently asked questions (FAQs)
• Submit a question directly to Technical Support
• Order Applied Biosystems user documents, MSDSs, certificates of analysis,
and other related documents
• Download PDF documents
• Obtain information about customer training
• Download software updates and patches
• Contact technical services by clicking the Care Center link.
In addition, the Support page provides access to worldwide telephone and fax
numbers to contact Applied Biosystems Technical Support and Sales facilities.
viii
Veriti™ Thermal Cycler User Guide
Preface
TVK Support
To send the temperature verification kit equipment for recalibration:
1. Use the address or Fax information below to request a quote from Alpha
Technics for a recalibration order:
• Mail: Alpha Technics
17151 Gillette Avenue
Irvine, Ca. 92614-5602
• Fax: (949)-271-2300
2. Ensure that the probe assembly has been decontaminated (see
“Decontaminating the Probe Assembly” on page 5-13).
3. Pack the digital thermometer and the probe assembly in the black case.
4. Create a shipping package with:
• Black case containing the digital thermometer and probe assembly
• Completed copy of the Certificate of Instrument Decontamination
• Payment for shipping/handling in one of the following forms:
– Purchase order
– Company letterhead with the words “verbal purchase order”
– Visa/MasterCard credit card information
• Your address and contact information:
– Billing address
– Return shipping address
– Name and phone number of a contact (person most familiar with the
thermometer)
Note: If payment is not included with the package, Alpha Technics bills you for
$150.00 plus a 10% administrative fee. The total for the purchase order is then
$165.00.
5. Send the package freight prepaid to Alpha Technics at the address in step 1.
Veriti™ Thermal Cycler User Guide
ix
Preface
x
Veriti™ Thermal Cycler User Guide
Safety and EMC Compliance Information
This section covers:
Safety Conventions Used in This Document. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
General Instrument Safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xv
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . xvii
Veriti™ Thermal Cycler User Guide
xi
Safety and EMC Compliance Information
Safety Conventions Used in This Document
Safety Alert
Words
Four safety alert words appear in Applied Biosystems user documentation at points
in the document where you need to be aware of relevant hazards. Each alert
word—IMPORTANT, CAUTION, WARNING, DANGER—implies a particular
level of observation or action, as defined below.
Definitions
IMPORTANT! – Indicates information that is necessary for proper instrument
operation, accurate chemistry kit use, or safe use of a chemical.
– Indicates a potentially hazardous situation that, if not avoided,
may result in minor or moderate injury. It may also be used to alert against unsafe
practices.
– Indicates a potentially hazardous situation that, if not avoided,
could result in death or serious injury.
– Indicates an imminently hazardous situation that, if not
avoided, will result in death or serious injury. This signal word is to be limited to the
most extreme situations.
Except for IMPORTANTs, each safety alert word in an Applied Biosystems
document appears with an open triangle figure that contains a hazard symbol. These
hazard symbols are identical to the hazard symbols that are affixed to Applied
Biosystems instruments (see “Safety Symbols” on page xiii).
Examples
The following examples show the use of safety alert words:
IMPORTANT! You must create a separate sample entry spreadsheet for each 96-well
plate.
The lamp is extremely hot. Do not touch the lamp until it has
cooled to room temperature.
CHEMICAL HAZARD. Formamide. Exposure causes eye,
skin, and respiratory tract irritation. It is a possible developmental and birth defect
hazard. Read the MSDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
ELECTRICAL HAZARD. Failure to ground the instrument
properly can lead to an electrical shock. Ground the instrument according to the
provided instructions.
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Veriti™ Thermal Cycler User Guide
Safety and EMC Compliance Information
Symbols on Instruments
Electrical
Symbols on
Instruments
The following table describes the electrical symbols that may be displayed on
Applied Biosystems instruments.
Symbol
Description
Indicates the On position of the main power switch.
Indicates the Off position of the main power switch.
Indicates a standby switch by which the instrument is
switched on to the Standby condition. Hazardous
voltage may be present if this switch is on standby.
Indicates the On/Off position of a push-push main
power switch.
Indicates a terminal that may be connected to the signal
ground reference of another instrument. This is not a
protected ground terminal.
Indicates a protective grounding terminal that must be
connected to earth ground before any other electrical
connections are made to the instrument.
Indicates a terminal that can receive or supply alternating
current or voltage.
Indicates a terminal that can receive or supply alternating
or direct current or voltage.
Safety Symbols
The following table describes the safety symbols that may be displayed on
Applied Biosystems instruments. Each symbol may appear by itself or with text that
explains the relevant hazard (see “Safety Labels on Instruments” on page xiv). These
safety symbols may also appear next to DANGERS, WARNINGS, and CAUTIONS
that occur in the text of this and other product-support documents.
Symbol
Description
Indicates that you should consult the manual for further
information and to proceed with appropriate caution.
Indicates the presence of an electrical shock hazard and
to proceed with appropriate caution.
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xiii
Safety and EMC Compliance Information
Symbol
Description
Indicates the presence of a hot surface or other
high-temperature hazard and to proceed with
appropriate caution.
Indicates the presence of a laser inside the instrument
and to proceed with appropriate caution.
Indicates the presence of moving parts and to proceed
with appropriate caution.
Environmental
Symbols on
Instruments
The following symbol applies to all Applied Biosystems electrical and electronic
products placed on the European market after August 13, 2005.
Symbol
Description
Do not dispose of this product as unsorted municipal
waste. Follow local municipal waste ordinances for
proper disposal provisions to reduce the environmental
impact of waste electrical and electronic equipment
(WEEE).
European Union customers:
Call your local Applied Biosystems Customer Service
office for equipment pick-up and recycling. See
http://www.appliedbiosystems.com for a list of
customer service offices in the European Union.
Safety Labels on Instruments
The following CAUTION, WARNING, and DANGER statements may be displayed
on Applied Biosystems instruments in combination with the safety symbols
described in the preceding section.
English
xiv
Francais
CAUTION Hazardous chemicals.
Read the Material Safety Data
Sheets (MSDSs) before handling.
ATTENTION Produits chimiques
dangeureux. Lire les fiches
techniques de sûreté de matériels
avant la manipulation des produits.
CAUTION Hazardous waste. Refer
to MSDS(s) and local regulations
for handling and disposal.
ATTENTION Déchets dangereux.
Lire les fiches techniques de
sûreté de matériels et la régulation
locale associées à la manipulation
et l'élimination des déchets.
WARNING Hot lamp.
AVERTISSEMENT Lampe
brûlante.
Veriti™ Thermal Cycler User Guide
Safety and EMC Compliance Information
English
Francais
WARNING Hot. Replace lamp with
an Applied Biosystems lamp.
AVERTISSEMENT Composants
brûlants. Remplacer la lampe par
une lampe Applied Biosystems.
CAUTION Hot surface.
ATTENTION Surface brûlante.
DANGER High voltage.
DANGER Haute tension.
WARNING To reduce the chance
of electrical shock, do not remove
covers that require tool access. No
user-serviceable parts are inside.
Refer servicing to
Applied Biosystems qualified
service personnel.
AVERTISSEMENT Pour éviter les
risques d'électrocution, ne pas
retirer les capots dont l'ouverture
nécessite l'utilisation d'outils.
L’instrument ne contient aucune
pièce réparable par l’utilisateur.
Toute intervention doit être
effectuée par le personnel de
service qualifié de
Applied Biosystems.
CAUTION Moving parts.
ATTENTION Parties mobiles.
General Instrument Safety
PHYSICAL INJURY HAZARD. Using the instrument in a
manner not specified by Applied Biosystems may result in personal injury or damage
to the instrument.
Moving and
Lifting the
Instrument
Operating the
Instrument
Cleaning or
Decontaminating
the Instrument
PHYSICAL INJURY HAZARD. The instrument is to be moved
and positioned only by the personnel or vendor specified in the applicable site
preparation guide. If you decide to lift or move the instrument after it has been
installed, do not attempt to lift or move the instrument without the assistance of
others, the use of appropriate moving equipment, and proper lifting techniques.
Improper lifting can cause painful and permanent back injury. Depending on the
weight, moving or lifting an instrument may require two or more persons.
Ensure that anyone who operates the instrument has:
• Received instructions in both general safety practices for laboratories and
specific safety practices for the instrument.
• Read and understood all applicable Material Safety Data Sheets (MSDSs). See
“About MSDSs” on page xvi.
Before using a cleaning or decontamination method other than
those recommended by the manufacturer, verify with the manufacturer that the
proposed method will not damage the equipment.
Veriti™ Thermal Cycler User Guide
xv
Safety and EMC Compliance Information
Chemical Safety
Chemical Hazard
Warning
About MSDSs
CHEMICAL HAZARD. Before handling any chemicals, refer
to the Material Safety Data Sheet (MSDS) provided by the manufacturer, and
observe all relevant precautions.
Chemical manufacturers supply current Material Safety Data Sheets (MSDSs) with
shipments of hazardous chemicals to new customers. They also provide MSDSs with
the first shipment of a hazardous chemical to a customer after an MSDS has been
updated. MSDSs provide the safety information you need to store, handle, transport,
and dispose of the chemicals safely.
Each time you receive a new MSDS packaged with a hazardous chemical, be sure to
replace the appropriate MSDS in your files.
Obtain MSDSs
from Applied
Biosystems
The MSDS for any chemical supplied by Applied Biosystems is available to you free
24 hours a day. To obtain MSDSs:
1. Go to www.appliedbiosystems.com, click Support, then click MSDS Search.
2. In the Keyword Search field, enter the chemical name, product name, MSDS
part number, or other information that appears in the MSDS of interest, then
click Search.
3. Find the MSDS of interest, click the link or right-click the MSDS title, then
select any of the following:
• Open – To view the MSDS
• Print Target – To print the MSDS
• Save Target As – To download a PDF version of the MSDS
Note: For the MSDSs of chemicals not distributed by Applied Biosystems,
contact the chemical manufacturer.
Chemical Safety
Guidelines
xvi
To minimize the hazards of chemicals:
• Read and understand the Material Safety Data Sheets (MSDSs) provided by the
chemical manufacturer before you store, handle, or work with any chemicals or
hazardous materials. (See “About MSDSs” on page xvi.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the MSDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood). For additional
safety guidelines, consult the MSDS.
• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the
manufacturer’s cleanup procedures as recommended in the MSDS.
• Comply with all local, state/provincial, or national laws and regulations related
to chemical storage, handling, and disposal.
Veriti™ Thermal Cycler User Guide
Safety and EMC Compliance Information
Chemical Waste Safety
Chemical Waste
Hazard
HAZARDOUS WASTE. Refer to Material Safety Data Sheets
and local regulations for handling and disposal.
Electrical Safety
ELECTRICAL SHOCK HAZARD. Severe electrical shock can
result from operating the Veriti Thermal Cycler without its instrument panels in
place. Do not remove instrument panels. High-voltage contacts are exposed when
instrument panels are removed from the instrument.
Fuses
FIRE HAZARD. Improper fuses or high-voltage supply can
damage the instrument wiring system and cause a fire. Before turning on the
instrument, verify that the fuses are properly installed and that the instrument voltage
matches the power supply in your laboratory.
FIRE HAZARD. For continued protection against the risk of
fire, replace fuses only with fuses of the type and rating specified for the instrument.
Power
Overvoltage
Rating
ELECTRICAL HAZARD. Grounding circuit continuity is vital
for the safe operation of equipment. Never operate equipment with the grounding
conductor disconnected. Use properly configured and approved line cords for the
voltage supply in your facility. Plug the system into a properly grounded receptacle
with adequate current capacity.
The Veriti Thermal Cycler has an installation (overvoltage) category of II, and is
classified as portable equipment
Physical Hazard Safety
Moving Parts
PHYSICAL INJURY HAZARD. Moving parts can crush and
cut. Keep hands clear of moving parts while operating the instrument. Disconnect
power before servicing the instrument.
Safety and Electromagnetic Compatibility (EMC)
Standards
This section provides information on:
•
•
•
•
U.S. and Canadian Safety Standards
Canadian EMC Standard
European Safety and EMC Standards
Australian EMC Standards
Veriti™ Thermal Cycler User Guide
xvii
Safety and EMC Compliance Information
U.S. and
Canadian Safety
Standards
The Veriti Thermal Cycler has been tested to and complies with standard:
UL 61010A-1/CAN/CSA C22.2 No. 1010.1-92, “Safety Requirements for Electrical
Equipment for Measurement, Control, and Laboratory Use, Part 1: General
Requirements.”
UL 61010A-2-010, “Particular Requirements for Laboratory Equipment for the
Heating of Materials.”
Canadian EMC
Standard
European Safety
and EMC
Standards
This instrument has been tested to and complies with ICES-001, Issue 3: “Industrial,
Scientific, and Medical Radio Frequency Generators.”
Safety
This instrument meets European requirements for safety (Low Voltage Directive
2006/95/EC). This instrument has been tested to and complies with standards
EN 61010-1:2001, “Safety Requirements for Electrical Equipment for Measurement,
Control and Laboratory Use, Part 1: General Requirements.”
EN 61010-2-010, “Particular Requirements for Laboratory Equipment for the
Heating of Materials.”
EN 61010-2-081, “Particular Requirements for Automatic and Semi-Automatic
Laboratory Equipment for Analysis and Other Purposes.”
EMC
This instrument meets European requirements for emission and immunity (EMC
Directive 2004/108/EC). This instrument has been tested to and complies with
standard EN 61326 (Group 1, Class B), “Electrical Equipment for Measurement,
Control and Laboratory Use – EMC Requirements.”
Australian EMC
Standards
xviii
This instrument has been tested to and complies with standard AS/NZS 2064,
“Limits and Methods Measurement of Electromagnetic Disturbance Characteristics
of Industrial, Scientific, and Medical (ISM) Radio-frequency Equipment.”
Veriti™ Thermal Cycler User Guide
System Overview
1
1
This chapter covers:
Introducing the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Using the Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Menu Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
About Run Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
About Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15
Veriti™ Thermal Cycler User Guide
1-1
Chapter 1
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
You control the Veriti Thermal Cycler using the touchscreen display and easy-to-use
interface. 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 1-1
The Applied Biosystems Veriti™ Thermal Cycler
This user guide provides information on how to maximize the capabilities of your
new 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 96Well Thermal Cyclers”.
1-2
Veriti™ Thermal Cycler User Guide
Chapter 1
System Overview
Detailed specifications for the Veriti Thermal Cycler are found in Appendix A,
“Instrument Specifications.”
Using the Touchscreen
You interact with the Veriti Thermal Cycler using a touchscreen.
Table 1 describes several buttons common to many of the touchscreens.
Table 1 Buttons in the Veriti™ Thermal Cycler 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.
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1-3
Chapter 1
System Overview
Entering Text
When you touch a field that requires the input of text, the text editor opens
(Figure 1-2).
Figure 1-2
The Veriti™ Thermal Cycler text editor
To...
Enter a lowercase letter
Touch...
A letter button.
Enter an uppercase letter
Caps, then the letter(s).
When you are done, touch Caps
again.
Enter punctuation or other symbols
Symbols, then the symbol(s).
When you are done, touch
Symbols again.
Remove the contents of the entire field
.
Delete the last letter
Close the editor and save any changes
1-4
Veriti™ Thermal Cycler User Guide
Chapter 1
Entering
Numerals
System Overview
When you touch a field that requires only numerical input, the numeric editor opens
(Figure 1-3).
Figure 1-3
The Veriti™ Thermal Cycler numeric editor
To...
Enter a number
Touch...
A number button.
The instrument automatically adds the
decimal point for those fields that include a
decimal point, such as a temperature value.
Colons (for entering times) and dashes (for
entering dates) are also automatically added.
Delete the last number
Remove the entire contents of the field
.
Close the editor and save any changes
.
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1-5
Chapter 1
System Overview
Menu Overview
The Main Menu
Screen
After you log in to the system, the Main Menu screen opens. This screen is the
starting point for operating the Veriti Thermal Cycler. 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 1-4
The Veriti™ Thermal Cycler Main Menu screen
In the Main Menu screen, touch:
• Browse/New Methods to view and work with all the run methods to which you
have access (see “Viewing a Run Method” on page 1-9).
• Settings Menu to access various instrument configuration options. If you have
administrative privileges, you access the Admin Menu screen from this screen
(see “The Settings Menu Screen” on page 1-7).
• 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 “The Tools Menu Screen” on page 1-8).
• 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 2-15).
• Log Off to log off the instrument. You can still log off 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.
1-6
Veriti™ Thermal Cycler User Guide
Chapter 1
The 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 1-5
The Admin Menu
Screen
System Overview
The Settings Menu screen, with the Admin Menu button shown
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 1-6
privileges
Veriti™ Thermal Cycler User Guide
The Admin Menu screen, available only to users with administrative
1-7
Chapter 1
System Overview
The Tools Menu
Screen
Use this screen to access various tools and instrument tests.
Figure 1-7
The Tools Menu screen, available to all users
For more information about the functions on the Tools Menu, see Chapter 5,
“Utilities.”
About Run Methods
What Is a Run
Method?
Predefined
Methods
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.
The Veriti Thermal Cycler firmware has ten predefined run methods:
•
•
•
•
•
•
•
•
•
•
•
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
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 C, “Predefined Run Methods.”
1-8
Veriti™ Thermal Cycler User Guide
Chapter 1
Viewing a Run
Method
System Overview
To view a run method:
1. In the Browse Run Methods screen, touch a run method to select it, then touch
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 – Touch the arrow buttons at the end of the
run method.
• View steps with ramp rates – Touch Options, then Ramp Rate. The fields
showing times update to show the corresponding ramp rates.
3. When you are done, touch
Veriti™ Thermal Cycler User Guide
to return to the Browse Run Methods screen.
1-9
Chapter 1
System Overview
Managing Run
Methods
To see the run methods in the current folder:
• In the Main Menu screen, touch Browse/New Methods.
The Browse Run Methods screen is displayed. The title includes the number of
run methods in parentheses.
Figure 1-8 The Browse Run Methods screen, showing the most recently
accessed run methods
To select a run method:
1. If a run method is already selected in the Browse Run Methods screen:
a. Touch the row for the selected method to deselect it.
b. Touch the row for the method of interest.
2. To select more than one method, touch each method.
Table 2 lists the administrative tasks you can perform for run methods.
Table 2 Managing run methods
If you want to...
Sort run methods by different
criteria
Do this...
Touch the title of the column with the criteria by which
you want to sort the run methods.
Touch the title a second time to sort in the opposite
order.
1-10
View more run methods in the
current folder
Touch
(Page Down).
View run methods in a different
folder
Touch
(folders). In the Manage Folders All screen
that opens, touch the folder you want to view.
Start a run
In the list of run methods, touch a run method to select
it, then touch Start Run (see “Performing a Run” on
page 3-18).
Veriti™ Thermal Cycler User Guide
Chapter 1
System Overview
Table 2 Managing run methods (continued)
If you want to...
Do this...
Create a new run method
Touch New (see “Creating a New Run Method” on
page 3-8).
View or edit a run method
In the list of run methods, touch the run method to
select it, then touch View/Edit (see “Editing Details” on
page 3-10).
Copy one or more run methods
In the list of run methods, touch each run method to
select it, then touch Copy (see “Copying a Run
Method” on page 1-11).
Print a run method
In the list of run methods, touch a run method to select
it, then touch Print (see “Printing a Run Method” on
page 1-12).
Delete one or more run methods
In the list of methods, touch each run method to select
it, then touch Delete (see “Deleting a Run Method” on
page 1-12).
Designate a run method as the
default
See “Designating a Run Method as the Default” on
page 1-12.
Create a shortcut to a run
method on the Main Menu
In the list of run methods, touch each run method to
select it, then touch
(Create Method Shortcut.)
See “Creating a Shortcut to a Run Method” on
page 1-13.
Copying a Run
Method
Back up run methods
See “Backing Up Run Methods and Other Settings” on
page 1-13.
Restore run methods that you
previously backed up
See “Restoring Run Methods and Other Settings” on
page 1-14.
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. Touch each run method to select it, then touch Copy.
4. In the Save Run Method screen:
a. If you are copying one method – touch Name, then rename the method,
and/or touch
(Folder) to save the run method to a different folder.
or
If you are copying more than one method – touch
(Folder) to save the
run methods to a different folder.
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Chapter 1
System Overview
b. As needed, touch 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. Touch 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 2-5.
1. In the Browse Run Methods screen, locate the run method you want to print.
2. Touch the run method to select it, then touch Print.
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. Touch the run method to select it, then touch Delete.
4. In the dialog box that opens, verify the deletion.
5. Touch 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 on page C-5) 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, touch Settings Menu.
3. In the Settings Menu screen, touch Set Default Method.
The Set the Default Run Method screen is displayed, with only the run methods
in the Shared folder displayed.
4. In the Set the Default Run Method, touch the run method you wish to designate
as the default, then touch Make Default. In the message box that opens, touch
OK.
The Settings Menu screen opens and the selected run method is now the default.
1-12
Veriti™ Thermal Cycler User Guide
Chapter 1
Creating a
Shortcut to a Run
Method
System Overview
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 2-15).
1. In the Browse Run Methods screen, touch one or more methods, then touch
(Create Method Shortcut).
2. In the message box that appears, touch 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 2-15.
Backing Up Run
Methods and
Other Settings
You can back up the instrument's 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.
USB Port
2. Log in as a user with Administrator access.
3. In the Main Menu screen, touch Settings Menu, then Admin Menu.
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Chapter 1
System Overview
4. In the Admin Menu screen, touch Back Up Methods & Settings.
The Back Up Method and Settings screen is displayed:
5. Touch 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. Touch OK, then touch
(Close) to return to the Admin Menu screen.
7. Remove the USB drive and store it in a safe place.
Restoring Run
Methods and
Other Settings
You can restore run methods and other settings from a USB drive to an instrument.
The restore feature can also be used to load run methods onto another instrument in
your lab.
To restore run methods and instrument settings:
1. Insert the USB drive containing the saved run methods and settings into the
USB port on the front of the instrument.
2. Open the About the Instrument screen in one of the following ways:
• Touch Log Off to return to the Login Options screen, then touch About
the Instrument.
• In the Main Menu screen, touch Settings Menu, then About the
Instrument.
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Veriti™ Thermal Cycler User Guide
Chapter 1
System Overview
The About the Instrument screen is displayed:
3. In the About the Instrument screen, touch Restore Methods & Settings, then
Yes in the message box.
The instrument copies all run methods, folders, user information, and other
instrument settings from the USB drive to the instrument, then displays a
message box when the restore is complete.
4. Remove the USB drive and store it in a safe place.
5. Toggle the switch on the back of the instrument to power off.
6. Toggle the switch again to power on the instrument.
IMPORTANT! If you restore information to an instrument that is different from the
instrument that provided the backup data and your instruments are on a network, you
should change the instrument’s name. See “Setting the Instrument Name” on
page 2-8.
About Folders
Each run method is saved in a folder. There are three folders available by default:
• Default – Run methods are stored here if you do not select another folder. Run
methods stored in this folder, run methods can be accessed, edited, run, and
deleted only by the user who created them. The Default folder has a blue button.
• Shared – Run methods can be accessed, edited, run, and deleted by any user. In
the Browse Folders screen, the Shared folder has a blue button.
• USB – This folder shows all run methods on the USB drive. If a USB drive is
present in the instrument, this button is blue, otherwise it is grey.
In addition, you may create up to nine custom folders. In a custom folder, run
methods can be accessed, edited, run, and deleted only by the user who created them.
In the Manage Folders screen, custom folders have a yellow button.
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Chapter 1
System Overview
You can create a new folder when you save a run method (see step 6 on page 3-9) or
you can create one by touching New in the Manage Folders screen.
Deleting Custom
Folders
You can delete any custom folder. When you delete a custom folder, all run methods
in that folder are also deleted.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Manage Folders.
3. In the Manage Folders screen, touch the button for the folder you want to delete,
then touch Delete.
4. Touch Yes in the dialog box that opens, then OK.
The folder is deleted.
5. Repeat steps 3 and 4 to delete other folders.
6. When you are done making changes to folders, touch
the Settings Menu screen.
Renaming
Custom Folders
(Close) to return to
You can rename any custom folder.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Manage Folders.
3. In the Manage Folders screen, touch the button for the folder you want to
rename, then touch Rename.
4. Enter up to 12 characters for the folder’s new name, then touch Done to return
to the Manage Folders screen.
5. Repeat steps 3 and 4 to rename any other folders.
6. When you are done making changes to folders, touch
the Settings Menu screen.
1-16
(Close) to return to
Veriti™ Thermal Cycler User Guide
Getting Started
2
2
This chapter covers:
Installing the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Setting Up the Veriti™ Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Veriti™ Thermal Cycler User Guide
2-1
Chapter 2
Getting Started
Installing the Veriti™ Thermal Cycler
Before You Start
Site
Requirements
System
Specifications
The Veriti™ Thermal Cycler is for indoor use. Ensure that the installation site:
•
•
•
•
Meets the spatial and weight requirements (see “System Specifications,” below)
Meets environmental requirements (see “Environmental Requirements,” below)
Is within 1 m (3 ft.) of a 800 VA power receptacle
Is away from water
Table 1 Physical dimensions, weight, and power consumption
Instrument
Footprint
Recommended
Clearance
Total
Length
48.5 cm
(19.1 in)
15.5 cm
(6.1 in) ‡
64 cm
(15.2 in)
Width
23.7 cm
(9.3 in)
0 cm
(0 in)
23.7 cm
(9.3 in)
Height §
40.0 cm
(15.7 in)
15.5 cm
(6.1 in) #
55.5 cm
(21.8 in)
Parameter
10.6 kg
(22.6 lbs)
Weight
Power
Consumption
800 VA – Maximum consumption
~260 VA – Average during thermal cycling
~10 VA – During sleep/standby
‡ At the rear of the instrument to ensure adequate airflow and cooling.
§ With the heated cover open
# Above the instrument to provide adequate space for opening the heated cover, as shown
below.
1 square. = 10 cm2 (3.94 in2)
2-2
Veriti™ Thermal Cycler User Guide
Chapter 2 Getting Started
Environmental Requirements
Temperature and
Humidity
Requirements
Ensure that the installation site is maintained under the following conditions:
Condition
Acceptable Range
Temperature
15 to 30 °C (59 to 86 °F)
Humidity
20 to 80% relative humidity, noncondensing
Avoid placing the instrument adjacent to heaters, cooling ducts, or in direct sunlight.
Fluctuations between day and night temperatures can cause system instability. Place
away from any equipment that vibrates, such as a refrigerator or centrifuge.
Pollution
Altitude
The Veriti Thermal Cycler has a Pollution Degree rating of 2. It may be installed in
an environment that has nonconductive pollutants only, such as dust particles or
wood chips. Typical environments with a Pollution Degree II rating are laboratories
and sales and commercial areas.
The safety of Veriti Thermal Cycler use was tested for altitudes up to 2000 ft.
Materials
Required
Materials
Optional
Protective
Hardware
• Scissors, pocket knife, or box cutter
• Compressed air
• Protective hardware, as appropriate (see below)
Applied Biosystems supports the use of the following devices to protect the Veriti
Thermal Cycler from damage resulting from electrical hazards and the resultant loss
of data. Before installing the system, decide what additional hardware (if any) you
want to install.
• Power line regulator (1.5-kVA)
• Surge protector/line conditioner (10-kVA)
• Uninterruptible power supply (1.5-kVA)
Unpacking the Veriti™ System
IMPORTANT! Save the packing materials and box in case you need to ship the
instrument to Applied Biosystems for service.
1. To unpack the Veriti™ System:
a. Cut the straps securing the instrument box.
b. Cut the tape securing the top flaps of the instrument crate, then open the
flaps.
c. Remove the Veriti™ System Accessories from the instrument and set them
aside.
d. Lift and remove the cover from the instrument crate.
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Getting Started
e. Remove the packing material from the Veriti™ System, then inspect the
instrument for shipping damage.
IMPORTANT! If the Veriti™ System is damaged, note the location and
appearance of the damage, then contact Applied Biosystems Technical Support
or your service representative (see “How to Obtain Support” on page viii).
2. Move the Veriti™ System to the desired installation site. Follow these
guidelines for lifting and moving:
• Make sure that you have a secure, comfortable grip.
• Keep your spine in a neutral position.
• Bend at the knees and lift with your legs.
• Do not lift and twist your torso at the same time.
3. Open the bag containing the Veriti™ System Accessories, then verify that it
contains:
• Applied Biosystems Veriti™ Thermal Cycler User Guide CD
• Cable, Power 13A/125V North America (PN 4382067)
• Cable, Power 10A/220V Europe (PN 4382068)
• Veriti™ System Starter Kit
Setting Up the Veriti™ System
1. Remove the packing material:
a. Open the Veriti™ System heated cover.
b. Remove the packing material from the sample block(s).
c. Using a can of compressed air, deliver a blast of air into each well of the
sample block(s) to remove any particles that may have collected during
transportation.
d. Close the heated cover.
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Veriti™ Thermal Cycler User Guide
Chapter 2 Getting Started
2. Connect the power cable to the Veriti™ System.
3. (Optional) Install any of the recommended protective devices (see “Optional
Protective Hardware” on page 2-3).
4. Connect the power cable to the 800 VA power source receptacle.
Connecting to a Network Printer
Requirements
The Veriti Thermal Cycler requires a printer that:
• Has an Ethernet port
• Supports the LPD/LPR protocol (often called a “TCP/IP printer”)
1. Plug the Ethernet cable into the Ethernet port on the back of the instrument.
2. Plug the other end of the cable into a network port.
You must also configure the instrument firmware with printer information
before you can print (see “Configuring the Instrument for a Printer” on
page 2-8).
Connecting Together Multiple Instruments
You Will Need
Connecting your Veriti Thermal Cycler to other Veriti Thermal Cyclers allows you
to use one instrument to control others. You can connect together up to 12
instruments.
To connect together multiple Veriti Thermal Cyclers, you need:
• An Ethernet cable for each Veriti Thermal Cycler
• A network switch
• A TCP/IP printer, if you want to print
For best results, do not connect the network switch to your laboratory’s network.
Communication between Veriti Thermal Cyclers works best on an isolated system,
free from interference by other network traffic.
Making the
Connections
1. Connect the Ethernet cable to the back of the thermal cycler and connect the
other end of the cable to the network switch.
2. Repeat step 1 for each thermal cycler.
3. Connect the printer to the network switch.
4. Power on the network switch.
5. For each thermal cycler, follow the instructions in “Setting the IP Address” on
page 2-7 and “Setting the Instrument Name” on page 2-8.
• When you set the instrument’s IP address, select Assign IP address
dynamically (using DHCP).
• Make sure each instrument name is unique.
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Getting Started
6. Follow the instructions in “Configuring the Instrument for a Printer” on
page 2-8.
7. Continue with “Powering On,” below, and “Setting Up the Veriti™ Thermal
Cycler” on page 2-7.
Powering On
1. Verify that the heated cover is closed.
2. Press the power button on the back left side of the instrument:
The instrument powers on and the Main Menu screen is displayed:
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Veriti™ Thermal Cycler User Guide
Chapter 2 Getting Started
Setting Up the Veriti™ Thermal Cycler
Recommended Instrument Settings
Before performing a run, be sure to set the following instrument settings:
•
•
•
•
Instrument IP address (page 2-7)
Instrument name (page 2-8)
Current date and time (page 2-8)
Printer information, if you want to print run methods or the run report
(page 2-8)
Optionally, you can also change the settings for:
•
•
•
•
Setting the IP
Address
User accounts and security (page 2-9)
Idle state temperatures for the cover and the sample block(s) (page 2-14)
Durations for pauses and stand-by (page 2-15)
“Shortcuts” to instrument functions (to be displayed on the Main Menu)
(page 2-15)
Note: If your instrument is not on a network, you do not need to set the IP address.
The IP address can be assigned dynamically by a computer on the network (using
DHCP) or set manually by entering a number in the IP Address screen.
Note: Ask your system administrator if the IP address is assigned statically or
dynamically. For static addresses, you need to know the IP address for the
instrument, the subnet mask, and the default gateway.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Admin Menu.
3. In the Admin Menu screen, touch Set IP Address.
4. In the IP Settings screen, set the IP address:
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Getting Started
• Dynamically – Touch Assign IP address dynamically (using DHCP). A
check mark appears when DHCP is selected.
or
• Manually – Touch Static, then enter the appropriate IP addresses for the
instrument, the subnet mask, and, optionally, the default gateway using the
numeric editor. Addresses are in the form of X.X.X.X, where each X is a 3digit number, from 001 to 255.
5. Touch Done, then OK to save your changes and return to the Admin Menu
screen.
Setting the
Instrument Name
By default the instrument name is set to the instrument serial number. You can
change the name to something more descriptive. The instrument name appears in the
About the Instrument and Run Report screens and, if you connect together multiple
instruments, in the Select Instruments screen.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Admin Menu.
3. In the Admin Menu screen, touch Set Instrument Name.
4. Touch the field to enter the new name.
Names cannot contain spaces and cannot be more than 24 alphanumeric
characters or, for numeric-only names, 10 characters.
5. Touch Yes next to Allow Remote Runs to make the instrument available for
remote runs (a run on this instrument can be started from another instrument);
otherwise touch No.
6. Touch Done, then OK to save your changes and return to the Admin Menu
screen.
Note: If you edit the Instrument Name field, you can still view the serial number in
the About the Instrument screen. You can access the About the Instrument screen
from either the Login screen or the Settings Menu screen.
Configuring the
Instrument for a
Printer
If you want to print the run report, test results, and/or a run method, you must
configure the instrument with information about the printer.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Configure Printer.
3. Touch the fields to set the printer’s name and IP address.
4. Touch Done to save your changes and return to the Settings Menu screen.
Setting the Date
and Time
The date and time appear in the run report and at the bottom of many of the screens
on the instrument.
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Admin Menu.
3. In the Admin Menu screen, touch Set Date & Time.
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Veriti™ Thermal Cycler User Guide
Chapter 2 Getting Started
4. To set the date, touch Date, then enter today’s date, using the format YYYYMM-DD. The instrument automatically enters the “-”.
5. To set the time, touch Time, enter the current time using the format HH:MM,
then touch AM or PM. The instrument automatically enters the “:”.
6. Touch Done, then OK to save your changes and return to the Admin Menu
screen.
Setting Up Instrument Security and User Accounts
By default, the Veriti Thermal Cycler has all security settings disabled, allowing
anyone to use the instrument and/or change instrument settings.
To change the security settings for the instrument:
1. Log in as a user with Administrator access.
2. In the Main Menu screen, touch Settings Menu.
3. In the Settings Menu screen, touch Admin Menu.
4. In the Admin Menu screen, touch Security.
5. To allow VeritiLink™ Remote Management Software to control this instrument,
touch Yes next to Allow VeritiLink Software Control.
6. To require each user to log in when using the instrument, touch Yes next to
Require Login.
7. To allow anyone to log in as a guest, touch Yes next to Enable Guest Account.
A guest user can perform runs, view and print run methods, and run tests. Also,
for run methods stored on a USB drive, a guest can create, view, edit, delete,
save, and print run methods.
A guest user cannot manage users or set instrument preferences.
8. To allow users to log in without entering a password, touch Yes next to Require
Password.
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Getting Started
9. Touch Done, then touch:
• Yes, to restart the instrument and have the changes take effect
immediately. Toggle the switch on the back of the instrument to power off
then toggle the switch again to power on the instrument. After you restart,
follow the instructions in “Adding Yourself, as a User” on page 2-10.
or
• No to have the changes take effect the next time the instrument is restarted
with the power switch on the back of the instrument.
Adding Users
Access Levels
Each user is assigned an access level that determines how he or she can interact with
the instrument. There are three access levels:
• Limited User – Can perform runs, view and print run methods, and run tests.
Cannot edit or create run methods, manage users, or set instrument preferences.
• User – Can perform runs, create, view, edit, delete, save and print run methods,
and run tests. Cannot manage users or set instrument preferences.
• Administrator – Can access all instrument functions, including setting security,
managing users and settings instrument preferences.
Adding Yourself,
as a User
If you set the instrument to require login, you need to use the default administrator
user name and password until you create your own user account.
To add yourself as a user:
1. In the opening screen, touch On, then Log In.
2. In the Log In screen, touch:
a. The User field, then enter admin.
b. The Password field, then enter password.
c. Log In.
3. In the Main Menu screen, touch Settings Menu.
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Chapter 2 Getting Started
4. In the Settings Menu screen, touch Admin Menu.
5. Follow the instructions in “Adding Users” to add yourself as a user. Make sure
you make yourself an Administrator.
Adding Users
To add a user:
1. Log in as a user with Administrator access.
2. In the Main Menu screen, touch Settings Menu.
3. In the Settings Menu screen, touch Admin Menu.
4. In the Admin Menu screen, touch Manage Users.
The Manage Users screen is displayed:
5. Touch Add User.
The Create New User Account screen is displayed:
6. Enter information for the new user. The required fields are User Name,
Password, Re-enter Password, and Permission Level.
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Getting Started
a. User Name must be between 5 and 15 characters, with no spaces.
b. Password must be at least 1 character.
c. Touch Set Access, then touch one of the following:
• Limited User
• User
• Administrator
d. Touch Done to close the Permission screen.
7. Touch Done, then OK to add the user account to the instrument.
The new user appears in the Manage Accounts screen.
8. When you finish, touch
Changing a User
(Close) to return to the Admin Menu screen.
To edit a user:
1. Log in as a user with Administrator access.
2. In the Main Menu screen, touch Settings Menu.
3. In the Settings Menu screen, touch Admin Menu.
4. In the Admin Menu screen, touch Manage Users.
The Manage Users screen is displayed:
5. In the list, touch the user in the list, then touch Edit User.
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Veriti™ Thermal Cycler User Guide
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The Edit User screen is displayed:
6. In the Edit User Account screen, make the required changes:
• Touch Phone and/or Email to edit the contents.
• Touch Set Access to change the access level for the user.
• Touch Set Password to change the password for the user.
7. Touch Done, then OK to return to the Manage Users screen.
8. When you finish, touch
Deleting a User
(Close) to return to the Admin Menu.
To delete a user:
1. Log in as a user with Administrator access.
2. In the Main Menu screen, touch Settings Menu.
3. In the Settings Menu screen, touch Admin Menu.
4. In the Admin Menu screen, touch Manage Users.
The Manage Accounts screen is displayed:
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Chapter 2
Getting Started
5. In the list, touch the user name for the account you want to delete, then touch
Delete User.
A confirmation message appears.
6. Touch OK to delete the user and any run methods or folders for that user, then
OK.
7. When you finish, touch
(Close) to return to the Admin Menu.
Setting Other Options
Table 2 lists additional options that can be adjusted or activated. These settings apply
to all users.
Table 2 Additional options (and their default values) for the Veriti Thermal Cycler
Option
Default Value
Idle temperatures for the cover and the sample
block(s)
Cover: 105 °C
Durations for pause and standby time-outs
Pause: 10 sec.
See
Page
2-14
Sample block(s): 25 °C
2-15
Standby: 1 min. 30 sec.
Shortcuts to appear on the Main Menu screen
Setting Idle
Temperatures for
the Block(s) and
Cover
None
2-15
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Set Idle Temperatures.
3. In the Idle State Temperatures screen, to set the temperatures for the sample
block(s) and the cover, touch:
2-14
Veriti™ Thermal Cycler User Guide
Chapter 2 Getting Started
a. Enabled to turn the option on. If this is disabled, the temperature for the
cover and/or block(s) is not maintained by the instrument and will
eventually come to room temperature.
b. The Temperature field, then enter the temperature. The temperature for
the cover must be between 4 and 99 °C.
4. Touch Done to save your changes and return to the Settings Menu screen.
Setting
Time-Outs
1. In the Main Menu screen, touch Settings Menu.
2. In the Settings Menu screen, touch Set Time-outs.
3. In the Set Time-Outs screen, touch Time-out, then enter the duration.
• Default Standby Time-Out sets the duration that the instrument is idle
before the touchscreen is turned off. Enter a duration of 00:00 if you do not
want the instrument to turn off the touchscreen.
• Default Pause Duration sets the duration the instrument pauses, after you
touch Pause during a run.
4. Touch Done, then OK to save your changes and return to the Settings Menu
screen.
Configuring Main
Menu Shortcuts
to Functions
You can add buttons to the Main Menu screen that allow you to go directly to various
instrument functions. When login is required, each user can configure his or her own
shortcut buttons; otherwise the shortcut buttons are displayed for all instrument
users.
You can also create shortcuts to run methods (see “Creating a Shortcut to a Run
Method” on page 1-13).
1. In the Main Menu screen, touch:
• Any button labeled Shortcut X (where X is a number).
or
• Settings Menu, then Configure Shortcuts.
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Getting Started
2. In the list of functions available as shortcuts in the Configure Shortcuts screen,
touch the functions to select them. Touch
(Page Up) and
(Page Down) to
scroll through the list.
3. Touch Done to return to the Settings Menu screen.
The selected shortcut(s) appear in the Main Menu screen.
Deleting Shortcuts
To delete a shortcut, follow the steps above, but uncheck the function to remove it
from the Main Menu. Any run methods for which there is a shortcut are shown at the
bottom of the list and can also be deleted.
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Veriti™ Thermal Cycler User Guide
Performing a Run
3
3
This chapter covers:
Selecting Disposables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Loading Samples into the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Creating a New Run Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Editing Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
Performing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
Monitoring a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-22
Viewing and Printing the Run Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
Removing the Samples from the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
Veriti™ Thermal Cycler User Guide
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Chapter 3
Performing a Run
Selecting Disposables
Use this section to determine the tube, sample tray, and plate configurations
appropriate for your thermal cycler and application.
• “Disposables for 96-Well Veriti™ Thermal Cyclers” on page 3-2
• “Disposables for the 384-Well Veriti™ Thermal Cycler” on page 3-4
• “Disposables for the 60-Well Veriti™ Thermal Cycler” on page 3-4
See Appendix B, “Disposables,” for part numbers for these items.
Disposables for 96-Well Veriti™ Thermal Cyclers
96-Well Tube
Configurations
IMPORTANT! The tray or the tray/retainer is required for the operation of the Veriti
Thermal Cycler.
You can use three different types of tube configurations to hold your samples, as
shown in Figure 3-1.
MicroAmp® Fast Reaction Tube with Cap (0.1-mL)
or
MicroAmp® Reaction Tube with Cap (0.2-mL)
MicroAmp® Reaction Tube (0.2-mL) with
MicroAmp™ 8-Cap Strip
GR1086c
Sedona
Tubes, Caps, Strip
GR1086c
MicroAmp™ Fast 8-Tube Strip (0.1-mL)
or
MicroAmp™ 8-Tube Strip (0.2-mL)
with MicroAmp™ 8-Cap Strip
Figure 3-1
Cyclers
3-2
Different tube configurations for use in 96-Well Veriti Thermal
Veriti™ Thermal Cycler User Guide
Chapter 3
96-Well Sample
Tray and Plate
Configurations
Run Vessel
MicroAmp™ Fast Optical
96-Well Reaction Plate
(0.1-mL)
™
The following table lists the possible sample tray and plate configurations.
IMPORTANT! The MicroAmp™ Splash Free 96-Well Base shown below is used
only when pipetting samples into tubes or trays. Do not place it in the sample
block(s).
Compatible Component
Illustration
MicroAmp™ Caps, 8-Cap
Strip
or
MicroAmp™ Clear Adhesive
Film (not shown)
MicroAmp™ 8-Cap Strip
GR2006
MicroAmp Optical
96-Well Reaction Plate
(0.2-mL)
Performing a Run
MicroAmp™ Fast Optical
96-Well Reaction Plate
(0.1-mL)
or
MicroAmp™ Optical
96-Well Reaction Plate
(0.2-mL)
MicroAmp™ Splash Free
96-Well Base
MicroAmp® Fast Reaction
Tube with Cap (0.1-mL)
96-Well Tray for VeriFlex™
Blocks
MicroAmp® Fast Reaction
Tube with Cap (0.1-mL)
or
MicroAmp® Reaction Tube
with Cap (0.2-mL)
GR2007
MicroAmp® Reaction Tube
with Cap (0.2-mL)
MicroAmp™ 96-Well Tray
for VeriFlex™ Blocks
MicroAmp™ Splash Free
96-Well Base
MicroAmp™ 8-Tube Strip
(0.2-mL)
or
MicroAmp® Reaction Tube
without Cap (0.2-mL)
MicroAmp™ 8-Cap Strip
and
MicroAmp™ 96-Well
Tray/Retainer Set for
Veriti™ Systems
MicroAmp™ 8-Cap Strip
MicroAmp™ 96-Well
Retainer
MicroAmp™ 8-Tube Strip
(0.2-mL)
or
MicroAmp® Reaction Tube
without Cap (0.2-mL)
GR2003
MicroAmp™ 96-Well Tray
for Veriti™ Systems
Veriti™ Thermal Cycler User Guide
MicroAmp™ Splash Free
96-Well Base
3-3
Chapter 3
Performing a Run
Disposables for the 384-Well Veriti™ Thermal Cycler
There is one plate configuration for the Veriti 384-Well Thermal Cycler, shown in
Figure 3-2, below. This uses the MicroAmp™ Optical 384-Well Reaction Plate.
Figure 3-2 MicroAmp™ Optical 384-Well Reaction Plate with MicroAmp™ Clear
Adhesive Cover
Disposables for the 60-Well Veriti™ Thermal Cycler
You can use three types of tubes to hold your samples, as shown in Figure 3-3.
GeneAmp® Thin-Walled Reaction Tube with Flat Cap (0.5-mL)
GeneAmp® Thin-Walled Reaction Tube with Domed Cap (0.5-mL)
or
GeneAmp® Thin-Walled Reaction Tube with Domed Cap,
Autoclaved (0.5-mL)
Figure 3-3
3-4
Different tubes for use in the Veriti™ 384-Well Thermal Cycler
Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
Loading Samples into the Instrument
See the appropriate section for your instrument:
• “Loading Samples in Veriti™ 96-Well Thermal Cyclers” on page 3-5
• “Loading Samples in the Veriti™ 384-Well Thermal Cycler” on page 3-6
• “Loading Samples in the Veriti™ 60-Well Thermal Cycler” on page 3-7
Loading Samples in Veriti™ 96-Well Thermal Cyclers
This section describes how to load samples in:
• Tubes with attached caps
• 96-well reaction plates
• 96-well tray/retainer assemblies
Loading Tubes
with Attached
Caps
There is no need to use mineral oil or glycerine in the sample wells or as a vapor
barrier over the PCR reaction mixture in the tubes. The MicroAmp® Reaction Tubes
fit tightly in the wells, and the heated cover exerts an even pressure on all tubes,
eliminating condensation on the tubes.
1. Set the 96-well tray on a splash-free 96-well base.
2. Place the reaction tubes in the tray.
3. Pipette the samples into the reaction tubes.
4. Cap the tubes.
5. See “Placing the Sample Tray or Plate onto the Sample Block(s)” on page 3-6.
Loading the
Reaction Plate
1. Place the reaction plate on a splash-free 96-well base.
2. Pipette the samples into the sample wells.
3. Cap the plates using the MicroAmp™ 8-Cap Strips, or cover the plates with
MicroAmp™ Clear Adhesive Film.
4. See “Placing the Sample Tray or Plate onto the Sample Block(s)” on page 3-6.
Loading Tubes
Without Caps
To load the 96-well tray/retainer:
1. Place the tray on the splash-free 96-well base.
2. Load tubes onto the tray using either single tubes or the 8-tube strips.
3. Place the retainer over the tubes.
4. Pipette the sample into the tubes.
5. Cap the tubes using a MicroAmp™ 8-Cap Strip.
6. See “Placing the Sample Tray or Plate onto the Sample Block(s)” on page 3-6.
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Chapter 3
Performing a Run
Placing the
Sample Tray or
Plate onto the
Sample Block(s)
The steps for placing the sample tray in the sample block(s) are the same for:
• A sample tray/retainer
• A sample tray without a retainer
• A 96-well plate.
1. Lift the sample tray from the splash-free 96-well base and place it in the sample
block(s).
2. Place the MicroAmp™ Tray or Plate onto the sample block(s) so that well A1 is
at the upper left corner of the tray, as shown below:
1
2
A
3
4
GR2380
7900
5
6
7
8
9
HS96_96Standard
A1
10
11
12
1
B
B
C
C
D
D
E
E
F
F
G
G
H
H
MicroAmp™ Fast Optical 96-Well
Reaction Plate (0.1-mL)
2
3
4
5
6
7
8
9
10
11
12
A
GR1070
A1
MicroAmp™ Optical 96-Well Reaction
Plate (0.2-mL)
IMPORTANT! Do not place the base in the sample block(s).
3. Close the heated cover.
Loading Samples in the Veriti™ 384-Well Thermal Cycler
This section describes how to load samples in 384-well reaction plates.
1. Pipette the samples into the sample wells.
2. Cover the plates with MicroAmp™ Clear Adhesive Film.
3. Place the MicroAmp™ Optical 384-Well Reaction Plate onto the sample
block(s) so that well A1 is at the upper left corner of the tray, as shown below:
GR2107
A1
MicroAmp™ Optical 384-Well Reaction Plate
4. Close the heated cover.
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
Loading Samples in the Veriti™ 60-Well Thermal Cycler
There is no need to use mineral oil or glycerine in the sample wells or as a vapor
barrier over the PCR reaction mixture in the tubes. The GeneAmp® Thin-Walled
Reaction Tubes fit tightly in the wells, and the heated cover exerts an even pressure
on all tubes, eliminating condensation on the tubes.
1. Pipette the samples into the reaction tubes.
2. Cap the tubes.
3. Place the GeneAmp® Thin-Walled Reaction Tubes with Flat or Domed Caps
(0.5 mL) onto the sample block(s).
4. Place the GeneAmp® Thermal Isolation Frame around the sample block(s).
5. Close the heated cover.
Veriti™ Thermal Cycler User Guide
3-7
Chapter 3
Performing a Run
Creating a New Run Method
1. In the Main Menu screen, touch Browse/New Methods.
2. In the Browse Run Methods screen, touch New.
The default run method is displayed in the Edit Run Method screen. (For
instructions on setting the default run method, see “Designating a Run Method
as the Default” on page 1-12.)
3. Edit the default run method as needed:
• Insert a stage (see “Adding a Stage” on page 3-10).
• Insert a step (see “Adding a Step” on page 3-11).
• Add an AutoDelta step (see “Creating an AutoDelta Step” on page 3-13).
• Add a pause (see “Adding a Pause” on page 3-15).
• Delete a step or stage (see “Deleting a Stage or Step” on page 3-15).
• For Veriti 96-Well Thermal Cyclers, you can add a step to program
different temperatures on the VeriFlex™ Blocks (see “Creating a VeriFlex™
Step” on page 3-16).
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
4. Touch Save & Exit to display the Save Run Method screen.
5. Touch Run Method to enter the name of the run method. Names can be up to
48 characters. Names may not contain any of the following characters:
%*?|;:,!@#$.()<>/\"'`~{}[]=+&^ (tab). Spaces, underscores, and dashes are
allowed.
6. Touch
(Folder) to select a folder in which to save the run method.
• To save the run method so that all users have access to it, touch Shared.
• To create a new folder for the run method, touch New Folder at the bottom
of the list, enter a name of up to 12 characters (no spaces), for the new
folder, then touch Done.
• To save the run method to the USB drive, touch USB (available only when
a USB drive is inserted in the instrument).
7. Touch Reaction Volume to enter the reaction volume. (You can change this
volume when you perform a run with this run method.)
8. Set the cover temperature, if any:
• Cover Temperature to enter the temperature for the heated cover.
or
• Do Not Heat Cover.
You can change this temperature when you perform a run with this run method.
9. Touch Notes, then enter any notes for the method.
10. Touch Save & Exit when you are done.
The Browse Run Methods screen is displayed.
Veriti™ Thermal Cycler User Guide
3-9
Chapter 3
Performing a Run
Editing Details
This section describes how to edit a run method by:
•
•
•
•
•
•
•
Adding a Stage
Adding a stage (page 3-10)
Adding a step (page 3-11)
Editing a temperature or a time (page 3-12)
Editing a ramp rate (page 3-12)
Creating an AutoDelta step (page 3-13)
Adding a pause (page 3-15)
Creating a step to program different temperatures on the VeriFlex Blocks
(page 3-16) (Available only on Veriti 96-Well Thermal Cyclers.)
The two types of run method stages are:
• Cycling – The steps in a cycling stage are repeated a specified number of times.
In general, the steps in a cycling stage are template denaturation, primer
annealing, and primer extension.
• Holding – The steps in a holding stage are not repeated.
To add a stage:
1. In the Edit Run Method screen, touch the stage name (at the top of the stage) to
select it. When a stage is selected, the area around the name is red.
2. Touch Add.
A copy of the selected stage is added to the run method.
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
3. For a cycling stage, edit the number of cycles as needed.
a. Touch the stage to select it.
b. Touch the cycles field (the box below the Stage Name) to select it:
c. Enter the number of cycles, then touch Done.
4. To change the temperature and/or time for any step in the stage, see “Editing
Temperature and Time” on page 3-12.
Adding a Step
1. In the Edit Run Method screen, touch anywhere in the column for a step to
select it.
When the step is selected, the column turns red:
2. Touch Add.
A copy of the selected step is added to the run method:
Veriti™ Thermal Cycler User Guide
3-11
Chapter 3
Performing a Run
3. To change the temperature and/or time for the step, see “Editing Temperature
and Time” on page 3-12.
Editing
Temperature and
Time
1. Touch any temperature field to select it, then edit the temperature as desired.
or
Touch any time field to select it, then edit the time as desired.
2. You can edit any other times, temperatures, (or the number of cycles for a stage)
without closing the editor.
a. Touch the field.
b. Touch the keys in the editor.
c. Repeat for any other field.
3. Touch Done to close the editor.
Editing Ramp
Rates
You can edit the rate at which the instrument ramps to the temperature for the step.
The default ramp rate is 100%.
Note: You cannot edit ramp rates for methods created using the Convert Method
wizard (see “Using GeneAmp® PCR System 9700 Run Methods” on page 5-2).
1. Touch a step to select it.
2. Touch Options, then Ramp Rate.
The field displaying time changes to display the ramp rate.
3. Touch the ramp field, then enter the desired ramp rate.
Ramp rates from 0.1 to 100% are valid.
4. Touch Done to close the editor.
The ramp rate symbol
100%.
3-12
appears next to any step with a ramp rate less than
Veriti™ Thermal Cycler User Guide
Chapter 3
Creating an
AutoDelta Step
Performing a Run
An AutoDelta step allows you to increase or decrease the temperature and/or change
the duration of the cycle during a cycling stage.
One use for an AutoDelta step is for touchdown PCR, a method in which the earliest
cycles have a high annealing temperature, followed by cycles where the annealing
temperature decreases slightly for each cycle. Touchdown PCR increases the
specificity of the PCR products. The high initial temperature favors more specific
annealing between the primer and the template. Because these fragments are further
amplified during subsequent cycles at lower temperatures, they outcompete the
nonspecific sequences to which the primers bind at lower temperatures.
Note: AutoDelta steps are allowed only in cycling stages.
To create an AutoDelta step:
1. Touch a step, then Options.
The options menu appears:
Veriti™ Thermal Cycler User Guide
3-13
Chapter 3
Performing a Run
2. In the Options menu, touch AutoDelta.
The Create an AutoDelta Step screen is displayed:
3. Touch Starting Cycle, then enter the cycle at which the AutoDelta step begins.
4. Select the parameter(s) to increment:
• Touch Delta Temperature, then enter the number of degrees that the
temperature changes for each cycle. To enter a temperature that decreases
with every cycle, touch + to change it to −. To enter a temperature that
increases, the button should show +.
and/or
• Touch Delta Time, then enter the minutes and seconds that the step
duration should change with each cycle. To enter a time that decreases with
each cycle, touch + to change it to −. To enter a time that increases, the
button should show +.
Note: Make sure the parameters you enter result in a final temperature greater
than 4.0 °C and less than 99.9 °C. Also, the Delta Time must be less than the
total time for the stage.
5. Touch OK to save the step and return to the screen that displays the run method.
The AutoDelta symbol
appears on the step with the AutoDelta step. In this
example, Step 2 in Stage 2 is an AutoDelta step:
3-14
Veriti™ Thermal Cycler User Guide
Chapter 3
Adding a Pause
Performing a Run
You can add a pause before any step in any cycling stage.
1. In the Edit Run Method screen, touch a step in a cycling stage to select it, then
touch Options.
2. In the Options Menu, touch Pause to display the Add a Pause Before a Step
dialog box:
3.
4. Enter:
• The first cycle in which the run will pause.
• The frequency of the pause.
• The duration of the pause, in mm:ss.
5. Touch Done to save the pause and return to editing the method.
The step preceded by the pause is indicated by the
below):
Deleting a Stage
or Step
(see Step 3 in Stage 3,
1. In the Edit Run Method screen, touch the stage or step to select it.
2. Touch Delete, then OK.
The stage or step is deleted from the run method.
Veriti™ Thermal Cycler User Guide
3-15
Chapter 3
Performing a Run
Creating a
VeriFlex™ Step
Note: This function is only available for the 96-well versions of the Veriti Thermal
Cycler.
The Veriti 96-Well Thermal Cyclers have six VeriFlex™ blocks. You can specify
temperatures for each VeriFlex™ block, or treat each VeriFlex™ block the same (the
default). The VeriFlex™ blocks can be used to provide up to six different temperature
zones for the 96 wells. A step that has different temperatures for different VeriFlex™
blocks is called a “VeriFlex™ step.” This feature is useful for quickly optimizing new
run methods.
To create a step with different temperatures for the VeriFlex™ blocks:
1. Touch a step, then Options.
The options menu appears:
2. In the Options menu, touch VeriFlex step.
The Create a VeriFlex Step screen is displayed:
z
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
3. Touch a temperature field, then enter the desired temperature. Temperatures for
neighboring VeriFlex™ blocks can be the same, but if they are not the same,
they must be at least 0.1 °C apart but no more than 5.0 °C apart. The maximum
temperature is 99.9 °C.
4. Repeat step 3 for each of the six VeriFlex™ blocks, then touch Done.
Note: To set each block to the same temperature, touch the desired temperature
field, then touch Apply Selected to All.
5. Depending on your instrument configuration, enter either a duration or a ramp
rate.
• Touch Time, enter the duration (in minutes and seconds), then touch Done.
or
• Touch Ramp Rate, enter the ramp rate (as a percentage value), then touch
Done.
The VeriFlex Step appears in the Edit Run Method screen, with the text “Zones”
in the temperature field.
Veriti™ Thermal Cycler User Guide
3-17
Chapter 3
Performing a Run
Performing a Run
Before You Begin
Prepare your samples and load the sample block(s) as described in “Loading Samples
into the Instrument” on page 3-5.
IMPORTANT! You can start a run on multiple instruments at the same time if your
instruments are on a network.
To start a run from the Main Menu screen:
1. Close the cover.
2. Touch Browse/New Methods.
3. Locate the run method you want to use (see “Viewing a Run Method” on
page 1-9), then touch the run method to select it.
4. Touch Start Run. The Run Parameters screen is displayed:
5. Touch Reaction Volume to edit the reaction volume. By default, the reaction
volume you entered when you saved the method is displayed.
Reaction volumes are specific to the type of instrument:
• Veriti 96-Well Fast Thermal Cycler: 5 to 40 µL
• Veriti 96-Well Thermal Cycler: 10 to 100 µL
• Veriti 384-Well Thermal Cycler: 5 to 30 µL
• Veriti 60-Well Thermal Cycler: 10 to 100 µL
6. Set the cover temperature:
• Cover Temperature to enter the temperature for the heated cover.
or
• Do Not Heat Cover.
7. Touch Run ID, and/or Notes, then enter the applicable information.
The default Run ID is YYYYMMDDHHMM, where “YYYYMMDD” is the
date and “HHMM” is the current time.
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
8. If you are making runs on:
• Only this instrument – Touch Start Run Now, then OK. The cover is
heated to the required temperature, then the run begins. When the run is
complete, the Run Report is displayed.
or
• Multiple instruments – Touch Start Multiple Runs. The Select
Instrument screen is displayed:
9. In the Select Instrument screen:
a. Touch the check box corresponding to each instrument on which you want
to perform the run. Only instruments that are compatible with the run
method are available. Incompatible instruments are indicated by
.
If you want to perform the run on this instrument, be sure to touch the
check box in the upper left corner of the screen.
b. Touch Start Run Now, then OK. The run method is sent to each selected
instrument, and, if no problems are encountered, the run begins.
After the run begins, you must interact with any remote instruments
directly if you want to make changes to the run method, pause, or stop the
run. When the runs are complete, the Run Reports are displayed on each
instrument.
Veriti™ Thermal Cycler User Guide
3-19
Chapter 3
Performing a Run
10. While the cover heats, the Cover Heating dialog box appears in the Run Monitor
screen:
If you want to:
• Start the run immediately, before the cover reaches the specified
temperature – Touch
(Skip).
• Stop the run – Touch
3-20
(Stop).
Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
Monitoring a Run
The Run Monitor
Screen
You can follow the status of a run using the Run Monitor screen (below):
A
B
C
D
E
H
F
G
Table 4 Elements of the Run Monitor screen
Location
in Figure
Element
Description
A
Run Monitor Button
and Status Bar
Displays the estimated temperature of the sample,
the temperature of the heated cover, the estimated
time remaining in the run, and the current stage.
B
Hot Icon
Indicates that the heated cover has achieved a
temperature sufficient to burn skin.
C
Stage Indicator
Indicates the stage that the Veriti™ System is
performing and the current cycle in that stage.
D
Step Temperature
Indicates the temperature for the step.
E
Hold Time
Indicates the time for the step. When this is the
current step, this field counts down.
F
Step Indicator
Indicates the step that the Veriti™ System is
performing.
G
Status Report
Displays the run status and any errors that occur
during the run. Touch the triangle to view the entire
report.
H
Arrow Button
Touch this to see the additional steps in the run
method.
See “Actions in the Run Monitor Screen During a Run” on page 3-22 for information
about what you can do during a run.
Veriti™ Thermal Cycler User Guide
3-21
Chapter 3
Performing a Run
Actions in the
Run Monitor
Screen During a
Run
During a run, the touchscreen is active, allowing you to perform the actions indicated
in the table.
Table 1 Actions in the Run Monitor Screen Allowed During a Run
To...
Do This
View other stages
Touch the scroll right and scroll left buttons.
Pause the run
Touch Pause Run (see “Pausing a Run” on
page 3-23).
View run method information
Touch View Method Information.
The information you entered in the Run
Parameters dialog box is shown.
Display the time for the run
Touch Display Method Time.
The elapsed time and time remaining for the
run are shown.
Skip to the next step
Touch SKIP.
Skip works only when the instrument is
holding.
Stop the run
Change the number of cycles
for a cycling stage
Touch STOP (see “Stopping a Run” on
page 3-23).
Touch the Cycle field then change the number of cycles
(see “Changing the Number of Cycles” on page 3-22).
Go to the Main Menu screen
View the Status Report
Changing the
Number of Cycles
Touch (Home). From the Main Menu Screen, you
can access most of the Veriti Thermal Cycler
functions while the run continues.
Touch
(Status).
You can change the number of cycles for a cycling stage while a run is in progress.
1. If needed, click the orange run monitor button to return to the run monitor
screen.
2. Touch the cycles field (below the Stage Name) for a cycling stage, then enter
the new value. You cannot:
• Edit a stage that is already complete.
• Enter a number that is smaller than the number of cycles that have already
been completed.
3. Touch Send to return to the Run Monitor screen.
The run continues, using the new number of cycles.
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Veriti™ Thermal Cycler User Guide
Chapter 3
Pausing a Run
Performing a Run
1. In the Run Monitor screen, touch Pause Run.
The Pause Run dialog box is displayed:
The run pauses for the duration set in the Set Time-Outs screen (see page 2-15).
In the Pause Run dialog box:
• Remaining Time shows the remaining time for the pause.
• Elapsed Time is continually updated to show the time the run has been in
process.
2. If you want to:
• Pause until the default pause has elapsed – Do nothing.
• Pause for a specific amount of time – Touch Edit Time, enter the duration
of the pause, then touch Done. The run resumes when the pause is
complete.
• Resume the run immediately – Touch Resume Run (to the left of the
dialog box).
Stopping a Run
In the Run Monitor screen, touch Stop, then OK.
The run stops and the Run Report opens.
Veriti™ Thermal Cycler User Guide
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Chapter 3
Performing a Run
Using the Run
Monitor Button
The Run Monitor button (Figure 3-1) is displayed at the top of the Run Monitor
screen. If you leave the Run Monitor screen during a run, this button also appears at
the top of all menu screens.
Figure 3-1
The Run Monitor button
You can touch the Run Monitor button to return to the Run Monitor screen at any
time.
If an error occurs during the run, the area showing the current stage, in the middle of
the button, is replaced by an alert icon:
Figure 3-2
If the Power Fails
Alert icon, shown in the Run Monitor button when an error occurs
If a power failure occurs during a run, the instrument attempts to continue the run
when the power returns. The run begins at the first step of the stage where the power
failed.
For example, the power fails during step 2 of the tenth cycle for a stage with three
steps and 20 cycles. After the power returns, the run starts at step 1 of the tenth cycle
and continues for 11 more cycles.
Note: If the time between the initial power failure and the time the power returns is
more than 18 hours, the run is not continued.
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Veriti™ Thermal Cycler User Guide
Chapter 3
Performing a Run
Viewing and Printing the Run Report
At the end of a run, the Run Report screen is displayed (below). If the last stage of
the run method is an infinite hold, you must touch Stop, then OK in the message box
before the Run Report is displayed.
You can also see the Run Report by touching View Last Run in the Tools Menu:
Note: The run report is saved only until the next run is finished.
• To print the run report, in the Run Report screen, touch Print.
If any errors occurred during the run, the error information is also printed.
• To save the run report to the USB drive, touch Save.
Removing the Samples from the Instrument
Grasp the sample tray/retainer assembly or reaction plate firmly with both hands and
gently rock it back and forth until the tubes (or plate) are free.
Sample caps may pop off if the cover is opened when the sample
block(s) temperature is above 27 °C.
Veriti™ Thermal Cycler User Guide
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Chapter 3
3-26
Performing a Run
Veriti™ Thermal Cycler User Guide
Troubleshooting
4
4
This chapter covers:
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Returning an Instrument for Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Veriti™ Thermal Cycler User Guide
4-1
Chapter 4
Troubleshooting
Troubleshooting
Use the following table to help troubleshoot problems with your Veriti™ Thermal
Cycler.
Problem
Possible Causes
Check and/or Remedy
Cooling rate too slow
• Peltier assembly failure
• Run the Cycle Performance Test.
Temperature does not match
specified temperature
• Instrument may require
calibration
• Run the Temperature Verification
Test.
Heating rate too slow
• Peltier failure
• Run the Cycle Performance Test.
Printing fails
• Printer incorrectly configured
on instrument
• Printer not connected to
network
• Instrument not connected to
network
• Ethernet cable bad
• Make sure the printer IP address on
the instrument matches the IP
address from the system
administrator.
• Is Ethernet cable connected to the
printer?
• Is Ethernet cable connected to the
instrument?
• Is network functioning?
• Try a different Ethernet cable.
Cycling time too long
• Peltier assembly failure
• Run the Cycle Performance Test.
When running on multiple
instruments, cannot see instruments
in “Select Instruments” screen
• Instrument(s) not connected to
network
• Switch powered off
• Ethernet cable bad
• IP address conflict
• Allow Remote Runs setting in
Instrument Name screen set to
No.
• Are all Ethernet cables connected to
the instruments?
• Are all Ethernet cables connected to
the network switch?
• Try a different Ethernet cable.
• Change the IP addresses on the
instruments.
• In Instrument Name screen, change
Allow Remote Runs to Yes.
No screen display
• Blown fuse
• Not connected to power source
• Check fuses.
• Is power switch on?
• Is power cord connected?
Screen display is missing characters
or is illegible
• LCD screen failure
• Request service.
Sample tubes melt during run
• Incompatible consumables
used
• Heated cover too hot
• Use recommended consumables
(see Appendix B, Disposables).
• Run the Heated Cover Verification
Test.
No response when you power on the
instrument
• Sample block(s) too hot
Heated cover stuck
• Cam, platen, or cover assembly
malfunctioning
• Request service
Heated cover not responsive
• Heated cover failure
• Run the Heated Cover Verification
Test.
4-2
Veriti™ Thermal Cycler User Guide
Chapter 4 Troubleshooting
Problem
Possible Causes
Check and/or Remedy
Cannot see Manage Users button in
Admin Menu screen
• Manage Users button is not
shown when instrument is
monitored by VeritiLink™
Remote Management Software
• Use VeritiLink Software to manage
user accounts
or
• Change Allow VeritiLink Software
Control to No in the Security screen
on the instrument.
Returning an Instrument for Service
Before returning an instrument for service, back up the run methods and instrument
settings, as described in “Backing Up Run Methods and Other Settings” on
page 1-13. This practice ensures that if the service center sends you a replacement
instrument, you can restore the run methods and other settings.
To return an instrument for service:
1. Contact your local customer care center or technical support group to obtain a
copy of the Certificate of Instrument Decontamination, a service notification, a
service call number, and, if required, packaging.
2. Decontaminate the instrument.
IMPORTANT! If the sample block(s) become contaminated with radioactivity,
use a commercially available decontaminant to remove the contamination. If the
block(s) cannot be decontaminated, the instrument cannot be returned to
Applied Biosystems for service.
3. Complete and sign a copy of the Certificate of Instrument Decontamination.
4. Fax the Certificate of Instrument Decontamination to the customer care center.
5. Pack the instrument in the provided packaging, without any accessories or
power cords. Include a hard copy of the Certificate of Instrument
Decontamination in the box.
Note: Repairs for instruments without the Certificate of Instrument
Decontamination are delayed.
6. Affix the provided postage to the box, then ship the instrument to the designated
facility.
The repair process requires 2 to 3 weeks.
Veriti™ Thermal Cycler User Guide
4-3
Chapter 4
4-4
Troubleshooting
Veriti™ Thermal Cycler User Guide
Utilities
5
5
This chapter covers:
Using GeneAmp® PCR System 9700 Run Methods. . . . . . . . . . . . . . . . . . . . . . . . 5-2
Upgrading System Firmware. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Calculating Melting Temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Viewing Instrument Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Restoring the Factory Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Running the Cycle Performance Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Tests Using the Temperature Verification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Veriti™ Thermal Cycler User Guide
5-1
Chapter 5
Utilities
Using GeneAmp® PCR System 9700 Run Methods
Note: This function is only available on Veriti 96-Well Thermal Cyclers.
The Veriti™ Thermal Cycler has a Convert Method tool to guide you through
importing existing run methods from a GeneAmp® PCR System 9700 thermal
cycler.
The tool is designed to create a method for the Veriti Thermal Cycler with ramp rates
that simulate those on the 9700 thermal cycler. Although the ramp rates may be
similar in the two methods, the results on the Veriti Thermal Cycler may differ from
those from the GeneAmp PCR System 9700 and, therefore, additional optimization
may be needed.
The available conversions are specific to the type of instrument:
• Veriti 96-Well Fast Thermal Cycler – Only 9700 Max Mode run methods can
be converted.
• Veriti 96-Well Thermal Cycler – Run methods in 9600 Emulation Mode or
9700 Max Mode can be converted.
Note: Only users who can save run methods (all users except Limited Users) have
access to this function.
To use a run method from a GeneAmp® PCR System 9700 thermal cycler:
1. Obtain a copy of the original method you want to convert, either by printing it
from the instrument or copying it manually to a piece of paper.
2. In the Main Menu screen, touch Tools Menu.
3. In the Tools Menu screen, touch Convert a Method to open the Convert
Method wizard:
4. Touch the check box next to the run method’s original format (9700 Max Mode
or 9600 Emulation Mode) then touch
(Next).
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Chapter 5
Utilities
5. In the second page, enter the original run method. You can include AutoDelta
steps, pauses, and VeriFlex™ steps, and you can edit the ramp rates:
Touch
(Next). when you are done.
6. In the Save Run Method page (below), enter a name and select a folder for the
run method. Names are limited to 16 characters. By default, the name begins
with “9700-Max-Mode-” or “9600-Mode-”, depending on the format selected in
step 4.
Also enter the reaction volume, the temperature for the heated cover (if any),
and any notes for this method.
When you finish, touch Save & Exit.
The Tools Menu is displayed.
Veriti™ Thermal Cycler User Guide
5-3
Chapter 5
Utilities
Note: You cannot edit the ramp rates in the method created by the Convert Method
wizard. This is indicated by “9600” or “9700M” in the Time field, when you choose
to view ramp rates rather than time (see Figure 5-1).
Figure 5-1
5-4
Converted run method, showing “9700M” as the ramp rate
Veriti™ Thermal Cycler User Guide
Chapter 5
Utilities
Upgrading System Firmware
About the
Upgrade
If Applied Biosystems provides a new version of the firmware for the Veriti Thermal
Cycler, you may be required to load the new firmware on the instrument.
You will need a USB drive and, if your instrument requires login, Administrator
access to upgrade the firmware.
IMPORTANT! You cannot upgrade the firmware while a run is in progress.
Upgrading the
Veriti Thermal
Cycler Firmware
1. Determine the version number of the existing firmware from the About the
Instrument screen.
a. Open the About the Instrument screen:
• Touch Log Off to return to the Login Options screen, then touch
About the Instrument.
or
• In the Main Menu screen, touch Settings Menu, then About the
Instrument.
The About the Instrument screen opens:
b. Record the version number of the firmware, then touch Done.
2. Determine the version number of the new firmware.
a. On a computer connected to the Internet, go to
www.appliedbiosystems.com.
b. Click Support, then Software Downloads.
c. Select Veriti Thermal Cycler in the list, then click Updates & Patches.
d. Find the appropriate file. If the version number is:
• The same as the current version (from step 1), you do not need to
upgrade the firmware.
• Different from the current version (from step 1), follow the steps
below to download and upgrade the firmware.
Veriti™ Thermal Cycler User Guide
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Chapter 5
Utilities
3. Download the new firmware to a USB drive:
a. Insert the USB drive into the USB port on the computer.
b. Click the link in the Software column to download the file. Select the USB
drive as the location for the saved file.
c. Remove the USB drive from the computer when the download is complete.
To upgrade the instrument with the new firmware:
1. Follow the instructions in “Backing Up Run Methods and Other Settings” on
page 1-13 to save your run methods and settings from the Veriti Thermal Cycler.
2. Insert the USB drive with the new firmware in the USB port on the front of the
Veriti Thermal Cycler,
3. Log in as a user with Administrator access.
4. In the Main Menu screen, touch Settings Menu.
5. In the Settings Menu screen, touch Admin Menu.
6. In the Admin Menu screen, touch Upgrade Firmware.
The Firmware Upgrade screen opens:
7. Touch Source File to display a list of the files on the USB drive. Veriti™ system
firmware files end with “.update”.
8. Touch the name of the file with the new firmware, then touch Select.
9. Touch Upgrade, then Yes.
When the upgrade process is complete, a message box opens.
10. Restart the instrument.
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Veriti™ Thermal Cycler User Guide
Chapter 5
Utilities
Calculating Melting Temperatures
To calculate the melting temperatures for a DNA primer pair:
1. In the Main Menu screen, touch Tools Menu.
2. In the Tools Menu screen, touch Calculate Tm to open the Tm Calculator
screen:
3. Enter the required information.
a. Touch Salt Concentration, then enter the salt concentration in mM.
b. Touch Primer Concentration, then enter the DNA concentration in µM.
c. Enter each primer sequence.
4. Touch Calculate.
The melting temperature for each primer is displayed:
Veriti™ Thermal Cycler User Guide
5-7
Chapter 5
Utilities
Viewing Instrument Statistics
The instrument records information about how it has been used. You can view this
information.
1. In the Main Menu screen, touch Tools Menu.
2. In the Tools Menu screen, touch Show Statistics.
The following statistics are shown:
• Total Cycles for Block(s) – The total number of cycles the instrument has
performed over its lifetime.
• Total Degrees for Block(s) – The total degrees the blocks) have climbed
over their lifetime. For example, if the sample block(s) were heated from
10 degrees to 30 degrees, for 3 cycles, the total degrees would be 60.
[3 × (30 − 10) = 60].
3. When you finish, touch Done to return to the Tools Menu screen.
Restoring the Factory Settings
You can reset the instrument to the default values for all instrument settings. When
you do this, the following are lost:
•
•
•
•
All run methods except the predefined methods listed in Appendix C
Any users and their custom folders
The instrument name and IP address
Any changes to time-outs, block idle temperatures, security settings, printer
settings, and any shortcuts to methods or functions
1. Log in as a user with Administrator access.
2. In the Main Menu screen, touch Settings Menu.
3. In the Settings Menu screen, touch Admin Menu.
5-8
Veriti™ Thermal Cycler User Guide
Chapter 5
Utilities
4. In the Admin Menu screen, touch Restore Factory Settings to open the Restore
Factory Settings screen:
5. In the Restore screen, touch Restore. The Restore Factory Settings dialog box is
displayed.
6. In the dialog box, touch:
• Yes to back up run methods and other settings before restoring the default
settings to the instrument. Insert a USB drive for the backup.
• No to restore the default settings, without first performing a back up.
Before the restore operation begins, you are prompted to confirm the
restore with a second dialog box.
IMPORTANT! Touching No erases all run methods, user accounts and
other settings from the instrument.
• Cancel to cancel the restore operation.
When the restore process is complete, a message box stating “Factory settings
have been restored.” opens.
7. Remove the USB drive, if present, then toggle the switch on the back of the
instrument to power off.
8. Toggle the switch again to power on the instrument and restart with the factory
default settings.
Veriti™ Thermal Cycler User Guide
5-9
Chapter 5
Utilities
Running the Cycle Performance Test
Use this test to verify that the sample block(s) are heating and cooling properly and
that the PCR cycling function operates properly.
Required
Materials
Procedure
The appropriate equipment for your instrument:
• Veriti 96-Well Fast Thermal Cycler: MicroAmp™Fast Optical 96-Well
Reaction Plate with Barcode (PN 4346906)
• Veriti 96-Well Thermal Cycler: MicroAmp™ Optical 96-Well Reaction Plate
(PN N8010560)
• Veriti 384-Well Thermal Cycler: MicroAmp™ Optical 384-Well Reaction Plate
(PN 4309849)
• Veriti 60-Well Thermal Cycler: GeneAmp® Thermal Isolation Frame
(PN 4308927)
This test takes 10 minutes to complete.
1. Place the reaction plate or thermal isolation frame in the instrument.
2. In the Main Menu screen, touch Tools Menu.
3. In the Tools Menu screen, touch Run Cycle Performance Test.
4. Follow the instructions on the screen to perform the test. The results are
displayed at the end of the test.
5. At the end of the test, touch:
• Print to print the results.
• Save to save the results to the USB drive.
The results are saved to the file CyclePEvents.txt.
6. If the test fails, repeat the procedure. Ensure that the heated cover is closed.
7. If the test fails again, contact Applied Biosystems Technical Support.
5-10
Veriti™ Thermal Cycler User Guide
Chapter 5
Utilities
Tests Using the Temperature Verification Kit
You need the Temperature Verification Kit to perform the:
• Heated Cover Verification
• Temperature Verification
• Temperature Nonuniformity Test
About the
Temperature
Verification Kit
The Temperature Verification Kit consists of:
• A probe – The appropriate size for the sample wells in your instrument. The
probe can be ordered separately or a part of a kit. (See page 6-6 for part numbers
for the probes.)
• Digital thermometer – Model 4690 Digital thermometer with 9 V battery
• Light mineral oil
• Cotton swabs
You need the appropriate model of the Temperature Verification Kit for your Veriti
Thermal Cycler, as shown below.
Veriti Thermal Cycler Model
For More
Information
Temperature Verification Kit
Part
Number
Veriti 96-Well Fast Thermal Cycler
(PN 4375305), with 0.1-mL sample
wells
0.1-mL Temperature Verification Kit
4373997
Veriti 96-Well Thermal Cycler
(PN 4375786), with 0.2-mL sample
wells
0.2-mL Temperature Verification Kit
4377669
Veriti 384-Well Thermal Cycler
(PN 4388444), with 0.02-mL sample
wells
0.02-mL Temperature Verification Kit
4385338
Veriti 60-Well Thermal Cycler
(PN 4384638), with 0.5-mL sample
wells
0.5-mL Temperature Verification Kit
4309924
See the Multiprobe Temperature Verification Kit User Guide (PN 4376864).
Running the Heated Cover Verification
Use this test to verify that the heated cover is within ±3 °C of the 105 °C set point.
Required
Materials
Procedure
The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model
(see table above).
This test takes 10 to 15 minutes to complete.
PHYSICAL INJURY HAZARD. Hot Surface. Use care when
working around the heated cover and sample block(s) to avoid being burned.
Veriti™ Thermal Cycler User Guide
5-11
Chapter 5
Utilities
1. In the Main Menu screen, touch Tools Menu.
2. In the Tools Menu screen, touch Run Heated Cover Verification.
3. Follow the instructions on the screen to perform the test.
4. At the end of the test, touch:
• Print to print the results.
• Save to save the results to the USB drive.
The results are saved to the file heatedCover.txt.
5. If the test fails, repeat the procedure. Ensure the:
• Probe plate is in the correct location. Probe 1 should be in well A5 during
this test.
• Cables are not damaged (no nicks, cuts or crimps) and are securely seated
in the digital thermometer and in the instrument.
• Heated cover is closed.
• Results are saved or printed.
6. If the test fails again, contact Applied Biosystems Technical Support.
Running the Temperature Verification
Use this test to verify that the average temperature for the sample block(s) is within
±0.25 °C of the set point temperature.
Required
Materials
The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model
(see table above).
Procedure
This test takes 25 to 30 minutes to complete, but you can cancel before it is complete.
PHYSICAL INJURY HAZARD. Hot Surface. Use care when
working around the heated cover and sample block(s) to avoid being burned.
1. In the Main Menu screen, touch Tools Menu.
2. In the Tools Menu screen, touch Run Temperature Verification.
3. Follow the instructions on the screen to perform the test.
4. At the end of the test, touch:
• Print to print the results.
• Save to save the results to the USB drive.
The results are saved to the file bcalevents.txt.
5. If the test fails, repeat the procedure. Ensure the:
• Probe is placed in the correct wells during the test.
• A drop of mineral oil is in each of the test wells.
• Cables are not damaged (no nicks, cuts or crimps) and are securely seated
in the digital thermometer and in the instrument.
• Results are saved or printed.
6. If the test fails again, contact Applied Biosystems Technical Support.
5-12
Veriti™ Thermal Cycler User Guide
Chapter 5
Utilities
Running the Temperature Nonuniformity Test
Use this test to verify that the sample well temperatures are within the threshold
temperature range.
Required
Materials
The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model
(see table above).
Procedure
This test takes 10 to 15 minutes to complete, but you can cancel before it is complete.
PHYSICAL INJURY HAZARD. Hot Surface. Use care when
working around the heated cover and sample block(s) to avoid being burned.
1. In the Main Menu screen, touch Tools Menu.
2. In the Tools Menu screen, touch Run TNU Test.
3. Follow the instructions on the screen to perform the test.
4. At the end of the test, touch:
• Print to print the results.
• Save to save the results to the USB drive.
The results are saved to the file tnuEvents.txt.
5. If the test fails, repeat the procedure. Ensure the:
• Cables are not damaged (no nicks, cuts or crimps) and are securely seated
in the digital thermometer and in the instrument.
• Heated cover is closed.
• Results are saved or printed.
6. If the test fails again, contact Applied Biosystems Technical Support.
TVK Recalibration
Applied Biosystems recommends that your Temperature Verification Kit be
recalibrated once a year.
Calibrating the thermometer and probe of the Temperature Verification Kit requires
that you:
• Decontaminate the probe assembly as described below.
• Send the equipment and the completed Certificate of Instrument
Decontamination to the manufacturer. See “TVK Support” on page ix.
Decontaminating
the Probe
Assembly
1. Contact your local customer care center or technical support group to obtain a
copy of the Certificate of Instrument Decontamination.
2. Gently wipe the probe cones with a cotton swab that has been moistened with
with a 1:10 v/v solution of 5.25% sodium hypochlorite (Chlorox bleach).
IMPORTANT! Do not submerge the probe in bleach solution. Do not
disassemble the probe assembly.
3. Complete the Certificate of Instrument Decontamination.
Veriti™ Thermal Cycler User Guide
5-13
Chapter 5
5-14
Utilities
Veriti™ Thermal Cycler User Guide
Maintenance
6
6
This chapter covers:
Scheduled Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
As-Needed Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Veriti™ Thermal Cycler User Guide
6-1
Chapter 6
Maintenance
Scheduled Maintenance
Run the following tests annually:
• Cycle Performance Test – page 5-10
• Heated Cover Verification – page 5-11
• Temperature Verification – page 5-12
As-Needed Maintenance
Tests
Run the Temperature Nonuniformity Test (see page 5-13).
Cleaning the Instrument
Preparation
Before cleaning the instrument:
1. Power off the Veriti™ Thermal Cycler, then remove the power cord.
2. Allow the instrument to cool until the heated cover and sample block(s) reach
room temperature.
Cleaning the
Touchscreen
Cleaning the
Sample Wells
Clean the touchscreen with any commercially available LCD cleaning product. Be
careful not to scratch the screen.
If you use any cleaning or decontamination method, except those recommended in
the manual, you risk damaging the equipment. Clean the sample wells once a month
or as needed.
Always wear protective glasses and gloves when servicing the
instrument. Also, make sure you disconnect the instrument from AC line power
before you begin any service procedure.
During instrument operation, the temperature of the heated cover
can be as high as 108 °C, and the temperature of the sample block(s) can be as high
as 100 °C. Before performing the procedure, keep hands away until the heated cover
and sample block(s) reach room temperature
To clean the sample wells:
1. Follow the steps in Preparation, above.
2. Open the heated cover.
3. Remove the sample tray from the sample block(s) and set it aside.
4. Use a cotton swab soaked in pure isopropanol to clean the sample wells
thoroughly. Make certain that the isopropanol has evaporated completely before
reloading a sample tray.
6-2
Veriti™ Thermal Cycler User Guide
Chapter 6 Maintenance
Decontaminating
the Sample Wells
If the sample wells become contaminated with any biological agents, clean the wells
thoroughly with a cotton swab soaked in 1:10 v/v dilution of 5.25% sodium
hypochlorite (Chlorox bleach).
Use bleach solution in moderation. Applied Biosystems recommends the use of
10% bleach solution for removing contamination from the Veriti™ instrument
sample block(s); excessive use of the solution, however, can corrode the sample
block(s) material. To prevent damage to the sample block(s):
• Avoid applying excessive amounts of bleach solution. If possible, instead of
using a squeeze bottle or soaked cloth, use an atomizer to deliver the solution to
the wells of the block(s).
• After treating with bleach solution, rinse the sample block(s) thoroughly using
deionized water.
Note: Removing residual bleach from the surfaces of the Veriti™ instrument using
water minimizes the long-term effects of bleach treatments.
If the sample block(s) become contaminated with radioactivity, use a commercially
available decontaminant to remove the contamination. If the block(s) cannot be
decontaminated, the instrument cannot be returned to Applied Biosystems for
service.
Cleaning the
Heated Cover
Clean the heated cover once a month or as needed.
During instrument operation, the temperature of the heated cover
can be as high as 108 °C, and the temperature of the sample block(s) can be as high
as 100 °C. Before performing the procedure, keep hands away until the heated cover
and sample block(s) reach room temperature.
To clean the heated cover:
1. Follow the steps in “Preparation” on page 6-2.
2. Open the heated cover.
3. Soak a cotton swab or piece of clean cloth with pure isopropanol and gently
wipe the heated platen.
CHEMICAL HAZARD. Isopropanol is a flammable
liquid and vapor. Exposure may cause eye, skin, and upper respiratory tract
irritation. Prolonged or repeated contact may dry skin and cause irritation.
Exposure may cause central nervous system effects such as drowsiness,
dizziness, and headache. Read the MSDS, and follow the handling instructions.
4. Remove any remaining isopropanol from the cover.
Note: If the platen becomes contaminated with amplified DNA, then raise the
heated cover to the cleaning position, wipe the platen with a cloth or cotton
swab soaked in bleach, then rinse with water.
Clean the heated platen once a month or as needed.
Veriti™ Thermal Cycler User Guide
6-3
Chapter 6
Maintenance
Decontaminating
the Heated Cover
If the heated cover become contaminated with amplified DNA, raise the heated cover
to the cleaning position and wipe the cover with a cloth or cotton swab soaked in 1:10
v/v dilution of 5.25% sodium hypochlorite (Chlorox bleach), then wipe the cover
with a damp cloth.
Replacing Fuses
Fuse Overview
The instrument has two 10 A Type M 250 V 5 × 20 mm fuses (PN 4377690).
FIRE HAZARD. For continued protection against the risk of
fire, replace fuses only with Listed and Certified fuses of the same type and rating as
those currently in the instrument.
ELECTRICAL HAZARD. To protect yourself against shock
hazards, use a properly wired three-terminal outlet. Do not use an adapter to a twoterminal outlet since this does not provide positive ground protection.
Instrument Configuration*
All configurations
Main Fuse Rating
Part Number
10 A
4377690
Acceptable AC line voltage tolerances: 100, 120, 220, 230 ±10%; 240 VAC
+6%/–10%, 50/60 Hz ± 1%
Required
Materials
Procedure
• Two 10 A Type M 250 V 5 × 20 mm fuses
• Fine flat-tip screwdriver
1. Turn off the instrument and disconnect the power cord from the back of the
instrument.
ELECTRICAL SHOCK HAZARD. Severe electrical
shock, which could cause physical injury or death, can result from working on
an instrument when the high voltage power supply is operating. To avoid
electrical shock, disconnect the power supply to the instrument, unplug the
power cord, and wait at least 1 minute before working on the instrument.
6-4
Veriti™ Thermal Cycler User Guide
Chapter 6 Maintenance
The fuses are in the power entry module:
Power entry module
Fuse compartment
2. Insert a small flat-tip screwdriver into the slot in the upper portion of the power
entry module, and open the door.
GR0961
3. Pull out the fuse compartment to inspect the two fuses in the fuse compartment:
4. Pull out the blown fuse(s) from the fuse compartment and replace with new
10 A Type M 250 V 5 × 20 mm fuses.
5. Place the fuse compartment back into the power entry module (there is only one
orientation) and close the door.
6. Press the door until it locks in place.
7. Connect the instrument power cord.
Veriti™ Thermal Cycler User Guide
6-5
Chapter 6
Maintenance
Parts List
Table 6-1
Kits and Spares
Part
PN
Kits
Temperature Verification Kit (0.1-mL)
4373997
Temperature Verification Kit (0.2-mL)
4377669
Temperature Verification Kit (0.02-mL)
4385338
Temperature Verification Kit (0.5-mL)
4309924
Spares
6-6
Cable, AC Power Supply
4374647
Cam, Left Side
4374274
Cam, Right Side
4374275
Foot, Rubber (Package of 4)
4375246
Fuse 10A Slo-Blo
4377690
Grill, Plastic Mold
4374178
Handle, Plastic
4374277
Handle, Rubber Grip
4374181
Heated Cover
4374276
Panel, Left
4374176
Panel, Rear (Heated Cover)
4374280
Panel, Right
4374175
Probe, Temperature Verification Kit (0.1-mL)
4375938
Probe, Temperature Verification Kit (0.2-mL)
4377670
Probe, Temperature Verification Kit (0.02-mL)
4308757
Probe, Temperature Verification Kit (0.5-mL)
4309925
Veriti™ Thermal Cycler User Guide
Instrument Specifications
A
A
This appendix covers:
System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Printer Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
Veriti™ Thermal Cycler User Guide
A-1
Chapter A Instrument Specifications
System Specifications
Physical
Dimensions and
Electrical
Specifications
Physical Dimensions
Width
23.7 cm (9.3 in)
Height
24.5 cm (9.6 in)
Depth
48.5 cm (19.1 in)
Weight
10.2 kg (22.5 lbs)
Electrical
Input Voltage
100 to 240 VAC 50/60 Hz
Max Power
AC Line Voltage Tolerances
Power and
Communication
Connections
10 A
100, 120, 220, 230 ±10%
240 VAC +6%/–10%, 50/60 Hz ± 1%
Table 1 Power and Communication
Port
Description
800 VA power cable
10/100 fast Ethernet port for a network connection
USB v1.0 port for a connection to an external USB drive
RS232 serial communication port for connecting the probe for the Temperature
Verification Kit
Figure A-1 Connections for power and communications on the Veriti™ Thermal
Cycler
A-2
Veriti™ Thermal Cycler User Guide
Chapter A Instrument Specifications
Sample
Temperature
Range
Touchscreen
Specifications
• Sample temperature range: +4 to +99.9 °C
• Temperature calibration accuracy: Traceable to National Institute of Standards
and Technology (NIST)
640 × 480 pixel LCD color display with full VGA resolution.
Sample Well
Specifications
No. of
Wells
Volume/Well
Veriti™ 96-Well Fast Thermal Cycler (PN 4375305)
96
0.1 mL
Veriti 96-Well Thermal Cycler (PN 4375786)
96
0.2 mL
Veriti 384-Well Thermal Cycler (PN 4388444)
384
0.02 mL
Veriti 60-Well Thermal Cycler (PN 4384638)
60
0.5 mL
Instrument Model
Printer Specifications
The Veriti Thermal Cycler requires a printer that:
• Has an Ethernet port
• Supports the LPD/LPR protocol (often called a “TCP/IP printer”)
Veriti™ Thermal Cycler User Guide
A-3
Chapter A Instrument Specifications
A-4
Veriti™ Thermal Cycler User Guide
Disposables
B
B
This appendix covers:
Disposables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-2
Other Supplies for Sample Handling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-4
Veriti™ Thermal Cycler User Guide
B-1
Chapter B
Disposables
Disposables
Table B-1 Disposables for the Veriti™ Thermal Cycler
Part Description
96-Well
(0.1-mL)
96-Well
(0.2-mL)
384-Well
(0.02-mL)
60-Well
(0.5-mL)
Part
Number
96-Well Plates
MicroAmp™ Fast 96-Well Reaction Plate (0.1 mL)
x
4346907
MicroAmp™ Fast Optical 96-Well Reaction Plate
with Barcode (0.1 mL)
x
4346906
x
4366932
MicroAmp™ Optical 96-Well Reaction Plate
x
N8010560
x
4316813
x
4306737
x
4326659
MicroAmp™ Optical 96-Well Reaction Plate with
Barcode and Optical Caps
x
403012
MicroAmp™ Optical 96-Well Reaction Plate with
Barcode and Optical Adhesive Films
x
4314320
MicroAmp™ Optical 96-Well Reaction Plate with
Barcode
MicroAmp™ Optical 384-Well Reaction Plate
x
4309849
MicroAmp™ Optical 384-Well Reaction Plate with
Barcode
x
4309849
x
4326270
x
4343814
12-Well Strips
MicroAmp™ 12-Cap Strip
MicroAmp™ 12-Cap Strip, Assorted Colors
x
x
N8010534
x
x
N8011534
x
x
N8010834
8-Well Strips
MicroAmp™ Fast 8-Tube Strip (0.1 mL)
x
4358293
MicroAmp™ 8-Tube Strip (0.2 mL)
x
N8010580
MicroAmp™ 8-Tube Strip, Assorted Colors (0.2
mL)
x
N8010838
MicroAmp™ Optical 8-Tube Strip (0.2 mL)
x
4316567
B-2
Veriti™ Thermal Cycler User Guide
Chapter B Disposables
Table B-1 Disposables for the Veriti™ Thermal Cycler (continued)
96-Well
(0.1-mL)
96-Well
(0.2-mL)
x
x
N8010535
x
x
N8011535
MicroAmp™ 8-Cap Strip, Assorted Colors
x
x
N8010835
MicroAmp™ Optical 8-Cap Strip
x
x
4323032
Part Description
MicroAmp™ 8-Cap Strip
384-Well
(0.02-mL)
60-Well
(0.5-mL)
Part
Number
Single Tubes
MicroAmp® Fast Reaction Tube with Cap (0.1 mL)
x
MicroAmp® Reaction Tube with Cap (0.2 mL)
4358297
x
N8010540
x
N8011540
MicroAmp® Reaction Tube with Cap, Assorted
Colors (0.2 mL)
x
N8010840
MicroAmp® Reaction Tube with Cap, Autoclaved
(0.2 mL)
x
N8010612
MicroAmp® Reaction Tube without Cap (0.2 mL)
x
N8010533
x
N8011533
MicroAmp® Reaction Tube without Cap, Assorted
Colors (0.2 mL)
x
N8010833
MicroAmp® Optical Tube without Cap (0.2 mL)
x
N8010933
GeneAmp® Thin-Walled Reaction Tube with Flat
Cap (0.5 mL)
x
N8010737
GeneAmp® Thin-Walled Reaction Tube with
Domed Cap (0.5 mL)
x
N801537
GeneAmp® Thin-Walled Reaction Tube with
Domed Cap, Autoclaved (0.5 mL)
x
N8010611
Seals & Covers
MicroAmp™ Clear Adhesive Film
x
x
x
4306311
MicroAmp™ Optical Adhesive Film
x
x
x
4360954
x
x
x
4311971
x
x
4313663
x
x
4379983
x
4381850
MicroAmp™ Optical Adhesive Film Kit
Reaction Trays
MicroAmp™ 96-Well Tray for VeriFlex™ Blocks
MicroAmp™ 96-Well Tray/Retainer Set for Veriti™
Systems
Veriti™ Thermal Cycler User Guide
B-3
Chapter B
Disposables
Other Supplies for Sample Handling
The following parts can simplify working with your samples and the Veriti™
Thermal Cycler.
Product
MicroAmp™ 96-Well Base
N8010531
MicroAmp™ Splash Free 96-Well Base
4312063
GeneAmp® Thermal Isolation Frame
4308927
MicroAmp™ Cap Installing Tool (Handle)
4330015
MicroAmp™ Multi-Removal Tool
4313950
MicroAmp™ Adhesive Film Applicator
4333183
MicroAmp™ Centrifuge Adapter
B-4
Part Number
N8013822
Veriti™ Thermal Cycler User Guide
Predefined Run Methods
C
C
This appendix covers:
Predefined Run Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C-2
Veriti™ Thermal Cycler User Guide
C-1
Chapter C Predefined Run Methods
Predefined Run Methods
The following run methods are supplied with the Veriti™ Thermal Cycler and are
stored in the Shared folder. These run methods are based on recommended protocols
from Applied Biosystems and should be considered as starting points for the
different applications. Your results may vary between instrument models, so some
optimization may be needed. Please note that the ramp rates of these methods are
100%.
•
•
•
•
•
•
•
•
•
•
•
AmpliCycle® Seq Run Method
AmpliTaq Gold® DNA Polymerase Run Method
AmpliTaq Gold® Fast PCR Run Method
BigDye® Kit Fast Run Method
BigDye® Kit Standard Run Method
Fast PCR Run Method
General PCR Run Method
LMS2 Run Method
Time Release Run Method
Touchdown PCR Run Method
XL PCR Run Method
These run methods cannot be edited or deleted, but if you save them with a different
name or to a different folder, you can edit them.
AmpliCycle® Seq Run Method
Use this run method to achieve clean sequence ladders from femtomole quantities of
template. The cycle sequencing process and the benefits of AmpliTaq® DNA
Polymerase, CS, are described in the product insert for the AmpliCycle® Sequencing
Kit (PN N8080175).
C-2
Veriti™ Thermal Cycler User Guide
Chapter C Predefined Run Methods
AmpliTaq Gold® DNA Polymerase Run Method
Use this run method for hot-start PCR in place of labor-intensive methods such as
manual hot-start or wax-bead-mediated hot-start techniques. The hot-start technique
helps to minimize the formation of primer-dimers or nonspecific products, thereby
increasing specificity and sensitivity of PCR. This run method specifies a pre-PCR
heat step for activation of AmpliTaq Gold® DNA Polymerase.
AmpliTaq Gold® Fast PCR Run Method
Use this run method for PCR with AmpliTaq Gold® Fast PCR Master Mix, UP to
produce optimal yield and specificity for a 500 bp amplicon. This run method is
optimized to generate template for DNA sequencing reactions and is only available
on Veriti™ 96-Well Thermal Cyclers.
Note: By default, the annealing temperature is set at 62 °C. Replace this temperature
with the melting temperature of the primer (see “Calculating Melting Temperatures”
on page 5-7).
Veriti™ Thermal Cycler User Guide
C-3
Chapter C Predefined Run Methods
BigDye® Kit Fast Run Method
Use this run method for cycle sequencing of dideoxy (Sanger) terminator sequencing
using ABI PRISM® BigDye® Terminator Cycle Sequence Ready Reaction Kits.
.
BigDye® Kit Standard Run Method
Use this run method, which consists of cycle-sequencing parameters for dideoxy
(Sanger) terminator sequencing, with ABI PRISM® BigDye® Terminator Cycle
Sequencing Ready Reaction Kits.
The pre-coded conditions in this run method are optimized for AmpliTaq® DNA
Polymerase, FS and the cycle sequencing reagents supplied with the BigDye®
Terminator kits.
C-4
Veriti™ Thermal Cycler User Guide
Chapter C Predefined Run Methods
Fast PCR Run Method
Use this run method for use with the GeneAmp® Fast PCR Master Mix. For more
information on how to convert your standard methods to Fast methods, refer to the
product literature for Fast PCR Master Mix available from
www.appliedbioystems.com.
General PCR Run Method
Use this run method for standard PCR use. This method is set as the default run
method for the Veriti Thermal Cycler.
Veriti™ Thermal Cycler User Guide
C-5
Chapter C Predefined Run Methods
LMS2 Run Method
Use this run method for ABI PRISM ® Linkage Mapping Set Version 2.5 (LMS2)
thermal cycling. Linkage Mapping Set Version 2 uses over 400 fluorescently labeled
PCR primer pairs for analysis of select microsatellite loci from the Généthon human
linkage map.
Time Release Run Method
Use this run method for use with AmpliTaq Gold® DNA Polymerase. This method
minimizes the pre-PCR activation step and adds a minimum of 10 additional cycles,
allowing for slow activation of the enzyme during cycling. This provides a simple
method where polymerase activity increases more slowly as product accumulates,
improving specificity.
C-6
Veriti™ Thermal Cycler User Guide
Chapter C Predefined Run Methods
Touchdown PCR Run Method
Use this run method if the optimal annealing temperature is not known. This method
incrementally decreases the annealing temperature in early cycles to maximize the
yield of specific products.
XL PCR Run Method
Use this run method for amplification of 5 to 40 kb PCR products using rTth DNA
Polymerase, XL and unique reaction conditions. By providing longer templates, XL
PCR complements technologies for rapid, long-range PCR. More complete genes
can be amplified in one reaction from known expressed sequences, allowing more
introns to be spanned. You can use XL PCR to amplify the control target (a 20.8-kb
product from Lambda DNA) supplied in the kit.
Veriti™ Thermal Cycler User Guide
C-7
Chapter C Predefined Run Methods
C-8
Veriti™ Thermal Cycler User Guide
Index
A
About the Instrument screen 5-5
adding
AutoDelta steps 3-13
folders 3-9
pauses in a run method 3-15
stages 3-10
steps 3-11
users 2-10
VeriFlex steps 3-16
Admin Menu screen 1-7
AmpliCycle run method C-2
AmpliTaq run methods C-3
appendices
Disposables B-1
Instrument Specifications A-1
Predefined Run Methods C-1
Applied Biosystems
contacting viii
customer feedback on documentation viii
Information Development department viii
Technical Support viii
assumptions for using this guide vii
AutoDelta step 3-13
cleaning
heated cover 6-3
sample wells 6-2
touchscreen 6-2
conventions
bold text vii
for describing menu commands vii
IMPORTANTS! vii
in this guide vii
italic text vii
Notes vii
safety xii
user attention words vii
creating
folders 3-9
run methods 3-8
shortcuts to instrument functions 2-15
shortcuts to run methods 1-13
users 2-10
customer feedback, on Applied Biosystems
documents viii
Cycle Performance Test 5-10
cycles
changing during a run 3-22
editing in a run method 3-11
B
D
backing up
before restoring to factory settings 5-9
run methods and settings 1-13
Big Dye Kit run methods C-4
bold text, when to use vii
DANGER, description xii
date, setting current 2-8
decontaminating
heated cover 6-4
sample wells 6-3
temperature verification kit 5-13
default administrator user name and password 2-10
default settings, restoring 5-8
deleting
folders 1-16
run methods 1-12
shortcuts 2-16
steps or stages 3-15
users 2-13
Display Method Time button 3-22
Disposables appendix B-1
documentation, related viii
C
calibrating, temperature verification kit 5-13
CAUTION, description xii
chapters
Getting Started 2-1
Maintenance 6-1
Performing a Run 3-1
System Overview 1-1
Troubleshooting 4-1
Utilities 5-1
chemical safety xvi
chemical waste safety xvii
Veriti™ Thermal Cycler User Guide
Index-1
Index
E
name 2-8
serial number 2-8
Instrument Specifications appendix A-1
IP address, setting 2-7
italic text, when to use vii
elapsed time for run, viewing 3-22
electrical safety xvii
electromagnetic compatibility standards. See EMC
standards
EMC standards xvii
Ethernet port A-2
L
F
linkage mapping C-6
LMS2 run method C-6
factory settings, restoring 5-8
FAST PCR run method C-5
firmware
upgrading 5-5
version number 5-5
folders
creating 3-9
deleting 1-16
renaming 1-16
fuses
changing 6-4
specification 6-4
G
General PCR run method C-5
Getting Started chapter 2-1
guest users 2-9
guidelines
chemical safety xvi
chemical waste disposal xvii
H
hazard icons. See safety symbols, on instruments
hazard symbols. See safety symbols, on instruments
hazards. See safety
heated cover
cleaning 6-3
decontaminating 6-4
setting temperature for a run 3-18
skipping heating during a run 3-20
temperature when idle 2-14
verification 5-11
Help system, accessing viii
Hot icon 3-21
I
IMPORTANT, description xii
Information Development department, contacting viii
installation category xvii
instrument operation, safety xv
instrument properties
IP address 2-7
Index-2
M
Main Menu screen 1-6
Maintenance chapter 6-1
maintenance schedule 6-2
Manage Users button missing 4-3
melting temperatures, calculating 5-7
menu commands, conventions for describing vii
moving parts, safety xvii
MSDSs
description xvi
MSDSs, obtaining viii
N
naming the instrument 2-8
O
online Help. See Help system
overvoltage category (rating) xvii
P
part numbers
disposable supplies B-2
Temperature Verification Kits 6-6
thermal cycler parts 6-6
password
default administrator 2-10
editing 2-13
logging in without 2-9
Pause Run button 3-22
pausing
before a step in run method 3-15
default duration 2-15
during a run 3-23
Performing a Run chapter 3-1
physical hazard safety xvii
power failure during a run 3-24
Predefined Run Methods appendix C-1
printing
run methods 1-12
run report 3-25
Veriti™ Thermal Cycler User Guide
Index
test results 5-10, 5-12, 5-13
troubleshooting 4-2
R
ramp rates
9600 5-4
9700M 5-4
editing 3-12
in converted methods 5-4
viewing 1-9
recalibrating, temperature verification kit 5-13
remaining time for run, viewing 3-22
remote runs
enabling 2-8
performing 3-19
troubleshooting 4-2
renaming
folders 1-16
instrument 2-8
restarting, after a power failure 3-24
restoring
factory settings 5-8
run methods and settings 1-14
returning an instrument, instructions 4-3
RS232 serial port A-2
rTth DNA polymerase C-7
run methods
backing up 1-13
copying 1-11
creating 3-8
deleting 1-12
predefined C-1
printing 1-12
restoring 1-14
saving 3-9
scrolling to left and right 3-22
shortcuts 1-13
Run Monitor screen 3-21
run parameters
entering 3-18
viewing during a run 3-22
run report
printing 3-25
saving 3-25
viewing most recent 3-25
S
safety
before operating the instrument xv
chemical xvi
chemical waste xvii
conventions xii
electrical xvii
guidelines xvi, xvii
Veriti™ Thermal Cycler User Guide
instrument operation xv
moving and lifting instrument xv
moving parts xvii
moving/lifting xv
physical hazard xvii
standards xvii
safety labels, on instruments xiv
safety standards xviii
safety symbols, on instruments xiii
sample block(s)
statistics 5-8
temperature when idle 2-14
sample wells
cleaning 6-2
decontaminating 6-3
specifications A-3
samples
loading 3-5
unloading 3-25
Sanger sequencing C-4
saving
run methods 3-9
run report 3-25
test results 5-10, 5-12, 5-13
serial number 2-8
serial port A-2
service, returning an instrument 4-3
Settings Menu screen 1-7
shortcuts
removing 2-16
to instrument functions 2-15
to run methods 1-13
SKIP button 3-22
stages
adding 3-10
cycling 3-10
deleting 3-15
holding 3-10
standards
EMC xvii
safety xvii
statistics, instrument 5-8
steps
adding 3-11
AutoDelta 3-13
deleting 3-15
pausing before 3-15
skipping during a run 3-22
VeriFlex 3-16
STOP button 3-22
symbols, safety xiii
System Overview chapter 1-1
Index-3
Index
T
V
Technical Support, contacting viii
Temperature Nonuniformity Test 5-13
temperature verification kit
contents 5-11
decontaminating 5-13
instructions for shipping ix
recalibrating 5-13
user guide 5-11
Temperature Verification Test 5-12
temperature, editing 3-12
test results files
bcalevents.txt 5-12
CyclePEvents.txt 5-10
heatedCover.txt 5-12
tnuEvents.txt 5-13
test results, saving 5-10, 5-12, 5-13
tests
Cycle Performance 5-10
Heated Cover Verification 5-11
Temperature Nonuniformity 5-13
Temperature Verification 5-12
text conventions vii
time
editing 3-12
elapsed for run 3-22
remaining for run 3-22
setting, current 2-8
Time Release run method C-6
Tools Menu screen 1-8
total cycles 5-8
total degrees for block(s) 5-8
Touchdown PCR
description 3-13
predefined run method C-7
touchscreen
cleaning 6-2
training, information on viii
Troubleshooting chapter 4-1
TVK See temperature verification kit 5-11
VeriFlex Blocks, description 1-2
VeriFlex Step, creating 3-16
VeritiLink Software 2-9
version number for firmware 5-5
View Method Information button 3-22
W
WARNING, description xii
X
XL PCR run method C-7
U
upgrading firmware 5-5
USB port A-2
user attention words, described vii
users
access levels 2-10
adding 2-10
changing 2-12
default administrator user name and password 2-10
deleting 2-13
Manage Users button missing 4-3
Utilities chapter 5-1
Index-4
Veriti™ Thermal Cycler User Guide
Worldwide Sales and Support
Applied Biosystems vast distribution and
service network, composed of highly trained
support and applications personnel,
reaches 150 countries on six continents.
For sales office locations and technical support,
please call our local office or refer to our
Web site at www.appliedbiosystems.com.
Applied Biosystems is committed to
providing the world’s leading technology
and information for life scientists.
Headquarters
850 Lincoln Centre Drive
Foster City, CA 94404 USA
Phone: +1 650.638.5800
Toll Free (In North America): +1 800.345.5224
Fax: +1 650.638.5884
06/2010
www.appliedbiosystems.com
Part Number 4375799 Rev. E