Applied Biosystems
9800 Fast Thermal Cycler User Guide Rev D Nov 2010
User Guide
48 Pages

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Applied Biosystems 9800 Fast Thermal Cycler With 96-Well Aluminum Sample Block Module
User Guide
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© Copyright 2006, 2010 Applied Biosystems. All rights reserved. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document. NOTICE TO PURCHASER: The combination of the Applied Biosystems 9800 Fast 96-Well Aluminum Sample Block Module with an Applied Biosystems 9800 Fast Thermal Cycler Base Module is licensed under US patent claims for thermal cycler apparatus, and counterpart patent claims in other countries. No other rights are conveyed expressly, by implication, or by estoppel. 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: Applied Biosystems is a registered trademark of Applied Biosystems or its subsidiaries in the U.S. and/or certain other countries. AB (Design) and Applera are trademarks of Applied Biosystems or its subsidiaries in the U.S. and/or certain other countries. All other trademarks are the sole property of their respective owners.
Part Number 4350087 Rev. D 06/2010
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Contents Preface Safety and EMC Compliance Information Chapter 1
Preparing, Loading, and Cleaning the 96-Well Sample Block Module About the Sample Block Module... 1-2 Sample Block Diagram... 1-2 The Sample Compartment... 1-3 Placing the Sample Block... 1-3 Heating and Cooling... 1-3 Electrical Requirements... 1-4 Part Numbers... 1-4 Loading Samples... 1-5 Loading the 96-Well Reaction Plate... 1-5 Placing the Sample Plate Onto the Sample Block... 1-5 Cleaning the Sample Block Module... 1-6 Cleaning the Sample Wells... 1-6 Cleaning the Heated Cover... 1-7
Chapter 2
Tests and Diagnostics The Calibration Verification Test... 2-2 Required Materials... 2-2 Threading the Probe Wire... 2-2 Setting Up the Probe Assembly... 2-2 Configuring the 9800 System... 2-3 Running the Test... 2-4 Evaluating the Results... 2-6 Ending the Test... 2-7 Calibration Verification Test Data Sheet... 2-8 Running the Temperature Non-Uniformity Test... 2-9 Equipment Required... 2-9 Setting Up the Probe Assembly... 2-9 Configuring the 9800 System... 2-10 Running the Test... 2-11
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Evaluating the Results... 2-14 Ending the Test... 2-14 Temperature Non-Uniformity Test Data Sheet... 2-15 System Performance Diagnostics... 2-16 Accessing the Tests... 2-16 Running The Rate Test... 2-16 Running the Cycle Test... 2-18
Index
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Preface How to Use This Guide Purpose of This Guide
Audience Text Conventions
The Applied Biosystems 9800 Fast Thermal Cycler with 96-Well Aluminum Sample Block Module User Guide provides instructions for preparing and loading samples and cleaning the module. It also gives test and diagnostic procedures and the necessary information for interpreting test results. This guide is intended for novice and experienced 9800 instrument users. 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 viii.
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Preface
How to Obtain More Information Related Documentation
Send Us Your Comments
The following related documents are shipped with the system: • Applied Biosystems 9800 Fast Thermal Cycler Base Module User Guide – Describes the Applied Biosystems 9800 Fast Thermal Cycler Base Module hardware and software and provides information on preparing, maintaining, and troubleshooting the system. 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 General Instrument Safety... xiv Chemical Safety...xv Chemical Waste Safety... xvi Electrical Safety... xvii Physical Hazard Safety... xviii Biological Hazard Safety... xix Laser Safety...xx Bar Code Scanner Laser Safety... xxi Workstation Safety... xxi Safety and Electromagnetic Compatibility (EMC) Standards... xxii
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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 ix). 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
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 x). 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.
x
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.
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.
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Safety Labels on Instruments
Instrument Warnings
Instrument Labels
ELECTRICAL HAZARD. Disconnect supply cord before opening. Grounding circuit continuity is vital for safe operation of equipment. Never operate equipment with grounding conductor disconnected. AVERTISSEMENT: Debrancher le cordon d’alimentation avant d’ouvrir la continuite des masses est essentielle. Pour un fonctionnement sans danger. Ne jamais utiliser l’equipment si le fil de terre n’est pas raccorde.
This symbol indicates the danger of burns, if precautions are not followed, due to the presence of heat in this area of the instrument. There may also be hot surfaces that can be easily touched. Attention. Surface chaude.
Electrical Safety Testing
Routine safety testing of analytical instruments (high potential voltage testing) may be required by various safety agencies. Testing should only be carried out by qualified personnel after seeking advice from the Applied Biosystems Service Department.
Danger of Burns
BURN HAZARD. During instrument operation, the temperature of the heated cover can be as high as 108 °C, and the temperature of the sample block can be as high as 100 °C. Before performing the procedure, keep hands away until the heated cover and sample block reach room temperature. AVERTISSEMENT: Surface chaude.
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General Instrument Safety Operating the Instrument
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 xii. 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.
Cleaning or Decontaminating the Instrument
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.
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.
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:
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Chemical Waste Safety
• 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
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 xii.) • 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.
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
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.
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• 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.
Waste Disposal
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.
Electrical Safety Fuses
ELECTRICAL SHOCK HAZARD. Improper fuses or highvoltage 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. Grounding circuit continuity is vital for the safe operation of equipment. Never operate equipment with the grounding conductor disconnected. 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.
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Biological Hazard Safety
Overvoltage Rating
The Applied Biosystems 9800 Fast 96-Well Aluminum Sample Block Module system has an installation (overvoltage) category of II, and is classified as portable equipment.
Biological Hazard Safety General Biohazard
BIOHAZARD. Biological samples such as tissues, body fluids, and blood of humans and other animals have the potential to transmit infectious diseases. Follow all applicable local, state/provincial, and/or national regulations. Wear appropriate protective eyewear, clothing, and gloves. Read and follow the guidelines in these publications: • U.S. Department of Health and Human Services guidelines published in Biosafety in Microbiological and Biomedical Laboratories (stock no. 017-04000547-4; http://bmbl.od.nih.gov) • Occupational Safety and Health Standards, Bloodborne Pathogens (29 CFR§1910.1030; http://www.access.gpo.gov/nara/cfr/ waisidx_01/29cfr1910a_01.html). Additional information about biohazard guidelines is available at: http://www.cdc.gov
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
This instrument has been tested to and complies with ICES-001, Issue 3: Industrial, Scientific, and Medical Radio Frequency Generators.
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European Safety and EMC Standards
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.” EMC
This instrument meets European requirements for emission and immunity (EMC Directive 89/336/EEC). 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.”
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Instrument Storage
Instrument Storage The 9800 system must be stored at a temperature between –20 °C and 60 °C (–4 °F and 140 °F) at altitudes ranging from 0 to 12,000 meters above sea level.
Sample Block Safe Operation Operating Precautions
The following precautions should be taken whenever you operate the Applied Biosystems 9800 Fast 96-Well Aluminum Sample Block Module. Read this section before you install the instrument. PHYSICAL INJURY HAZARD. To protect yourself against burns, do not open the heated cover or touch the sample block when the word Hot displays on the screen. This indicates a block temperature above 50 °C. IMPORTANT! To protect your samples and to guarantee the best temperature uniformity, keep the heated cover closed at all times, except when loading or unloading samples.
Routine Maintenance
Maintain your instrument in good working order. In the event that the instrument has been subjected to adverse environmental conditions (such as fire, flood, earthquake, and so forth), a service inspection of the instrument should be made to insure safe operation.
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 9800 system 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! This instrument is not designed for operation with the heated cover retracted when running at 4°C. If the cover is retracted and the instrument runs at 4°C, water condensation may be excessive in the block area.
Pollution The instrument has a pollution degree rating of 2 and may be installed in an environment that has nonconductive pollutants only.
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Preparing, Loading, and Cleaning the 96-Well Sample Block Module 1
1
This chapter covers: About the Sample Block Module... 1-2 Loading Samples... 1-5 Cleaning the Sample Block Module... 1-6
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1-1
Chapter 1 Preparing, Loading, and Cleaning the 96-Well Sample Block Module
About the Sample Block Module Sample Block Diagram
The following are two diagrams of the top and bottom of a sample block module. A release lever at the rear of the interchangeable sample block releases the sample block module from the base unit.
Release lever
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