Applied Biosystems
2720 Thermal Cycler User Guide Rev F Nov 2010
User Guide
122 Pages

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Applied Biosystems 2720 Thermal Cycler For Amplification of Nucleic Acids
User Guide
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. © Copyright 2010 Applied Biosystems. All rights reserved. NOTICE TO PURCHASER: Label License The Applied Biosystems 2720 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. The trademarks mentioned herein are the property of Applied Biosystems or their respective owners. AmpErase, AmpliTaq, AmpliTaq Gold, EnviroAmp, GeneAmp, and TaqMan are registered trademarks of Roche Molecular Systems, Inc. Microsoft, Windows, and Windows NT are registered trademarks of Microsoft Corporation. The information contained in this document is subject to change without notice. Produced 11/2010 Part Number 4359453, Rev. F
Contents 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...x Symbols on Instruments... xi Safety Labels on Instruments...xii Instrument Warnings Diagram... xiv General Instrument Safety...xv Chemical Safety...xv Chemical Waste Safety...xvii Electrical Safety... xviii Laboratory Environmental Requirements...xx Physical Hazard Safety...xx Safety and Electromagnetic Compatibility (EMC) Standards... xxi
1 System Overview Overview... 1-1 Introducing the Applied Biosystems 2720 Thermal Cycler... 1-2 About the Control Panel... 1-4 Overview of Functions... 1-5 Introducing an Important Screen... 1-6
2 Getting Started Overview... 2-1 Powering On... 2-2 Adding Yourself as a User... 2-3 Creating a Method... 2-5 Editing Your Method... 2-7 Starting and Stopping a Run... 2-8 More Features... 2-10
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3 Runs Overview... 3-1 Using Disposables... 3-2 Loading Samples... 3-5 Starting a Run... 3-7 Pausing or Stopping a Run... 3-9 Reviewing the History of a Run... 3-11 When a Run Completes... 3-13
4 Methods and Users Overview... 4-1 Adding, Changing, or Deleting a User Name... 4-2 Creating a Method... 4-6 Changing a Method Using Advanced Features... 4-9 Handling Methods... 4-18
5 Utilities Overview... 5-1 Configuring the Instrument... 5-2 Upgrading System Firmware... 5-4 Connecting to a Printer... 5-5 Calculating the Melting Temperature... 5-6 Running Hardware Diagnostics... 5-7 Running the Calibration Verification Test... 5-9 Running the Temperature Non-Uniformity Test... 5-9 Running System Performance Diagnostics... 5-10
6 Maintenance Overview... 6-1 Cleaning the Instrument... 6-2 Replacing Fuses... 6-4
7 Troubleshooting Overview... 7-1 If There’s a Power Failure... 7-2 Display Screen Error Messages... 7-3 Troubleshooting Information... 7-6
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A Specifications Overview...A-1 System Specifications...A-2 Control Panel Specifications...A-2 Sample Temperature Information...A-3 Printer Specifications...A-3
B Supplied Methods Overview...B-1 About the Methods...B-2
C Screen Flowcharts Overview...C-1 Run...C-2 Stop or End of Run...C-3 Create/Edit...C-4 User...C-5 Utilities...C-6 Diagnostics...C-7 Upgrade...C-8
D Instrument Warranty Information Overview...D-1 Computer Configuration...D-2 Limited Product Warranty...D-2 Damages, Claims, and Returns...D-4
Index
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Preface How to Use This Guide Purpose of This Guide
Text Conventions
The Applied Biosystems 2720 Thermal Cycler User Manual describes how to use the Applied Biosystems 2720 Thermal Cycler. The user manual provides information about performing runs and diagnostic tests as well as maintenance and troubleshooting. This guide uses the following conventions: • Bold 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 bracket (>) separates successive commands you select from a drop-down or shortcut menu. For example: Select File > Open > Spot 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 size of the column affects the run time. Note: The Calibrate function is also available in the Control Console. IMPORTANT! To verify your client connection to the database, you need a valid Oracle user ID and password. IMPORTANT! You must create a separate Sample Entry Spreadsheet for each 96-well
plate.
Safety Alert Words
Safety alert words also appear in user documentation. For more information, see “Safety Alert Words” on page x.
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How to Obtain More Information Related Documentation
The following related document is shipped with the system: Applied Biosystems 2720 Thermal Cycler Quick Reference Card – Provides brief, step-by-step procedures for using the 2720 Thermal Cycler. It is designed to help you quickly learn to use the 2720 Thermal Cycler. Portable document format (PDF) versions of this guide and the Applied Biosystems 2720 Thermal Cycler Quick Reference Card are also available on the Applied Biosystems 2720 Thermal Cycler software installation CD. Note: For additional documentation, see “How to Obtain Support” below.
Send Us Your Comments
Applied Biosystems welcomes your comments and suggestions for improving its user documents. You can e-mail your comments to: [email protected]
How to Obtain Support 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 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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Safety and EMC Compliance Information This section includes the following topics: Safety Conventions Used in This Document...x Symbols on Instruments... xi Safety Labels on Instruments... xii Instrument Warnings Diagram... xiv General Instrument Safety...xv Chemical Safety...xv Chemical Waste Safety... xvii Electrical Safety... xviii Laboratory Environmental Requirements...xx Physical Hazard Safety...xx Safety and Electromagnetic Compatibility (EMC) Standards... xxi
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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 icons that are affixed to Applied Biosystems instruments (see “Safety Symbols” on page xi). Examples
The following examples show the use of safety alert words: IMPORTANT! You must create a separate a 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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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 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 in combination with text that explains the relevant hazard (see “Safety Labels on Instruments” on page xii). 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.
Indicates the presence of a hot surface or other high-temperature hazard and to proceed with appropriate caution.
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Symbol
Description 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.
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. Read the waste profile (if any) in the site preparation guide for this instrument before handling or disposal.
ATTENTION Déchets dangereux. Lire les renseignements sur les déchets avant de les manipuler ou de les éliminer.
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.
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.
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English
Francais
DANGER Class <<3B, 3R, or 4>> laser radiation present when open and interlock defeated. Avoid direct exposure to laser beam.
DANGER Class <<3B, 3R, or 4>> rayonnement laser en cas d’ouverture et d’une neutralisation des dispositifs de sécurité. Eviter toute exposition directe avec le faisceau.
DANGER Class <<3B, 3R, or 4>> laser radiation when open. Avoid direct exposure to laser beam.
DANGER Class <<3B, 3R, or 4>> rayonnement laser en cas d’ouverture. Eviter toute exposition directe avec le faisceau.
DANGER Class <<2 (II), 3B, 3R, or 4>> laser radiation present when open and interlock defeated. Do not stare directly into the beam
DANGER de Class <<2 (II), 3B, 3R, or 4>> rayonnement laser en cas d'ouverture et d'une neutralisation des dispositifs de securite. Eviter toute exposition directe avec le faisceau.
DANGER Class <<2 (II), 3B, 3R, or 4>> laser radiation present when open. Do not stare directly into the beam.
DANGER de Class <<2 (II), 3B, 3R, or 4>> rayonnement laser en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
DANGER Class <<2 (II), 3B, 3R, or 4>> LED when open and interlock defeated. Do not stare directly into the beam.
DANGER de Class <<2 (II), 3B, 3R, or 4>> LED en cas d'ouverture et d'une neutralisation des dispositifs de securite. Eviter toute exposition directe avec le faisceau.
DANGER Class <<2 (II), 3B, 3R, or 4>> LED when open. Do not stare directly into the beam.
DANGER de Class <<2 (II), 3B, 3R, or 4>> LED en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
CAUTION Moving parts.
ATTENTION Parties mobiles.
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Instrument Warnings Diagram
GR1987
The following diagram shows where the hazards and warnings labels are located on rear of the 2720 Thermal Cycler.
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General Instrument Safety Moving and Lifting the Instrument
Operating 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. PHYSICAL INJURY HAZARD. Use this instrument as specified by Applied Biosystems. Using this instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument.
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. CHEMICAL HAZARD. All chemicals in the instrument, including liquid in the lines, are potentially hazardous. Always determine what chemicals have been used in the instrument before changing reagents or instrument components. Wear appropriate eyewear, protective clothing, and gloves when working on the instrument. CHEMICAL HAZARD. Four-liter reagent and waste bottles can crack and leak. Each 4-liter bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles. CHEMICAL STORAGE HAZARD. Never collect or store waste in a glass container because of the risk of breaking or shattering. Reagent and waste bottles can crack and leak. Each waste bottle should be secured in a lowdensity polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles.
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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.
Obtaining MSDSs
You can obtain from Applied Biosystems the MSDS for any chemical supplied by Applied Biosystems. This service is free and available 24 hours a day. To obtain MSDSs: 1. Go to https://docs.appliedbiosystems.com/msdssearch.html 2. In the Search field, type in the chemical name, part number, or other information that appears in the MSDS of interest. Select the language of your choice, then click Search. 3. Find the document of interest, right-click the document title, then select any of the following: • Open – To view the document • Print Target – To print the document • Save Target As – To download a PDF version of the document to a destination that you choose 4. To have a copy of a document sent by fax or e-mail, select Fax or Email to the left of the document title in the Search Results page, then click RETRIEVE DOCUMENTS at the end of the document list. 5. After you enter the required information, click View/Deliver Selected Documents Now.
Chemical Safety Guidelines
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To minimize the hazards of chemicals: • Read and understand the Material Safety Data Sheets (MSDS) 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 on the MSDS. • Comply with all local, state/provincial, or national laws and regulations related to chemical storage, handling, and disposal.
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Chemical Waste Safety Chemical Waste Hazard
HAZARDOUS WASTE. Refer to Material Safety Data Sheets and local regulations for handling and disposal. CHEMICAL WASTE HAZARD. Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury, illness, or death. CHEMICAL STORAGE HAZARD. Never collect or store waste in a glass container because of the risk of breaking or shattering. Reagent and waste bottles can crack and leak. Each waste bottle should be secured in a lowdensity polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles.
Chemical Waste Safety Guidelines
Waste Disposal
To minimize the hazards of chemical waste: • Read and understand the Material Safety Data Sheets (MSDSs) provided by the manufacturers of the chemicals in the waste container before you store, handle, or dispose of chemical waste. • Provide primary and secondary waste containers. (A primary waste container holds the immediate waste. A secondary container contains spills or leaks from the primary container. Both containers must be compatible with the waste material and meet federal, state, and local requirements for container storage.) • 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. • Handle chemical wastes in a fume hood. • After emptying the waste container, seal it with the cap provided. • Dispose of the contents of the waste tray and waste bottle in accordance with good laboratory practices and local, state/provincial, or national environmental and health regulations. If potentially hazardous waste is generated when you operate the instrument, you must: • Characterize (by analysis if necessary) the waste generated by the particular applications, reagents, and substrates used in your laboratory. • Ensure the health and safety of all personnel in your laboratory. • Ensure that the instrument waste is stored, transferred, transported, and disposed of according to all local, state/provincial, and/or national regulations. IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal limitations may apply.
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Electrical Safety Grounding
ELECTRICAL SHOCK HAZARD. Grounding circuit continuity is vital for the safe operation of equipment. Never operate equipment with the grounding conductor disconnected ELECTRICAL SHOCK HAZARD. Do not use an adapter to a two-terminal outlet since this does not provide positive ground protection.
Fuses
ELECTRICAL SHOCK HAZARD. Improper fuses or line 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
ELECTRICAL HAZARD. Use properly configured and approved line cords for the voltage supply in your facility. ELECTRICAL HAZARD. Plug the system into a properly grounded receptacle with adequate current capacity.
Overvoltage Rating
Electrical Shock Hazard
The Applied Biosystems 2720 Thermal Cycler has an installation (overvoltage) category of II, and is classified as portable equipment
ELECTRICAL SHOCK HAZARD. 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 réduire le risque de chocs électriques, ne pas ouvrir les couvercies si un outil est nécessaire. Ne contient aucune pièce pouvant être réparée par l’utilisateur. Confier le dépannage au personnel qualifié de Applied Biosystems.
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GR1987
Power on/off switch 3-pronged power cord receptacle
The 3-pronged power cord and receptacle at the instrument rear contain the grounding connector.
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. AVERTISSEMENT: Pour éviter les chocs électriques, débrancher le cordon d’alimentation avant le dépannage. Fire Hazard 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. AVERTISSEMENT: Afin d’assurer la protection contre les risques d’incendie, remplacer uniquement par un fusible de méme type et de méme courant nominal.
GR1987
Fuse compartment
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Laboratory Environmental Requirements Temperature, Humidity, and Environment
IMPORTANT This instrument is designed for indoor use. IMPORTANT Do not operate in a Cold Room or a refrigerated area. The 2720 Thermal Cycler will operate safely when the ambient temperature is 5 °C to 40 °C (41 °F to 104 °F) and will meet performance specifications when the ambient temperature is 15 °C to 30 °C and the ambient relative humidity is 20 to 80%. These specifications have been calculated for altitudes between 0 and 2,000 meters.
FIRE HAZARD. This instrument is not designed for operation in an explosive environment. Do not place the instrument close to potentially explosive materials or objects.
IMPORTANT The instrument should be stored between –20 °C and 60 °C (–4 °F and 140 °F) at altitudes between 0 and 12,000 meters. Note This instrument is able to withstand transient overvoltage according to Installation Category II as defined in IEC 1010-1.
Physical Hazard Safety Moving Parts
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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.
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Danger of Burns
PHYSICAL INJURY HAZARD. Hot Surface. Use care when working around this area to avoid being burned by hot components.
GR1988
AVERTISSEMENT: Surface chaude.
Safety and Electromagnetic Compatibility (EMC) Standards This section provides information on: • • • •
U.S. and Canadian Safety Standards
U.S. and Canadian Safety Standards Canadian EMC Standard European Safety and EMC Standards Australian EMC Standards
This instrument has been tested to and complies with standard UL 3101-1, “Safety Requirements for Electrical Equipment for Laboratory Use, Part 1: General Requirements.” This instrument has been tested to and complies with standard CSA 1010.1, “Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements.”
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 73/23/EEC). 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” and EN 61010-2-010, “Particular Requirements for Laboratory Equipment for the Heating of Materials.”
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