Applied Biosystems
Veriti User Guide Rev E June 2010
User Guide
124 Pages

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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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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
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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.
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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.
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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.
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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
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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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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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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.
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English
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.
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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.
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Safety and EMC Compliance Information
Chemical Safety Chemical Hazard Warning
CHEMICAL HAZARD. Before handling any chemicals, refer to the Material Safety Data Sheet (MSDS) provided by the manufacturer, and observe all relevant precautions.
About MSDSs
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
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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
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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
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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
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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”.
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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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