Applied Biosystems
3130 and 3130xl Getting Started Guide Rev D June 2010
Getting Started Guide
196 Pages

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Page 1
Applied Biosystems 3130/3130xl Genetic Analyzers
Getting Started Guide
Preparing the Instrument
Performing Spatial Calibration
Performing Spectral Calibration
Autoanalysis and Sequencing Analysis Software
Autoanalysis and SeqScape Software
Autoanalysis and Fragment Analysis
Running the Instrument
© Copyright 2007, 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: This instrument is Authorized for use in DNA sequencing and fragment analysis. This authorization is included in the purchase price of this instrument and corresponds to the up-front fee component of a license under process claims of U.S. patents and under all process claims for DNA sequence and fragment analysis of U.S. patents now or hereafter owned or licensable by Applied Biosystems for which an Authorization is required, and under corresponding process claims in foreign counterparts of the foregoing for which an Authorization is required. The running royalty component of licenses may be purchased from Applied Biosystems or obtained by using Authorized reagents purchased from Authorized suppliers in accordance with the label rights accompanying such reagents. Purchase of this instrument does not itself convey to the purchaser a complete license or right to perform the above processes. This instrument is also licensed under U.S. patents and apparatus and system claims in foreign counterparts thereof. No rights are granted expressly, by implication or by estoppel under composition claims or under other process or system claims owned or licensable by Applied Biosystems. For more information regarding licenses, please contact the Director of Licensing at Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. Applied Biosystems 3130 Genetic Analyzer: Covered by one or more of U.S. Pats. Nos. RE37,606; RE37,941. Applied Biosystems 3130xl Genetic Analyzer: Covered by one or more of U.S. Pats. Nos. RE37,606; RE37,941. NOTICE TO PURCHASER The purchase price of this Applied Biosystems 3130/3130xl Genetic Analyzer includes a grant of a limited, non-transferable license under U.S. patent claims and method claims of its foreign counterparts, and element claims of its foreign counterparts, to use this particular instrument for electrophoresis methods employing fluorescence as a means of detection. No other licenses or rights are hereby conveyed either expressly, by implication, or estoppel including, but not limited to, any claims to a composition. The Applied Biosystems 3130 and 3130xl Genetic Analyzers includes patented technology licensed from Hitachi, Ltd. as part of a strategic partnership between Applied Biosystems and Hitachi, Ltd., as well as patented technology of Applied Biosystems. Trademarks Applied Biosystems, AmpFlSTR, BigDye, Cofiler, GeneMapper, Identifiler, Profiler, Profiler Plus ID, SeqScape, SGM Plus, SNaPshot, and StockMarks are registered trademarks and AB (Design), Applera, Hi-Di, KB, POP, POP-4, POP-6, POP-7, SEfiler, and Yfiler are trademarks of Applied Biosystems or its subsidiaries in the U.S. and/or certain other countries. Dell is a registered trademark of Dell Computer Corporation. Microsoft, Windows, and Windows XP are registered trademarks of the Microsoft Corporation in the United States and other countries. Oracle is a registered trademark of the Oracle Corporation.
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Part Number 4352715 Rev. D 06/2010
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All other trademarks are the sole property of their respective owners.
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Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide Workflow
Start the system
Start Data Collection software
Check polymer block, select capillary array, and polymer
Performing a Spatial Calibration
Start a spatial calibration run
Evaluate spatial calibration profile
Accept or reject spatial calibration
Chapter 3
Performing a Spectral Calibration
Prepare spectral calibration chemistry
Create a spectral instrument protocol
Perform a spectral calibration
Chapter 4
Autoanalysis and Sequencing Analysis Software
Create protocols for automated sequencing analysis
Create a Sequencing Analysis Plate Record
Chapter 5
Autoanalysis and SeqScape® Software
Create protocols for automated SeqScape Software analysis
Create a SeqScape Software Plate Record
Chapter 6
Autoanalysis and Fragment Analysis
Create protocols for automated fragment analysis
Create a GeneMapper® Software Plate Record
Chapter 7
Running the Instrument
Chapter 1
Preparing the Instrument
Chapter 2
Prepare samples and plate assemblies
Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide
Place Plate onto Autosampler
Link the Plate
Prepare buffer and fill reservoirs
Evaluate the spectral calibration data
Schedule a run
Run the instrument
Activate a spectral calibration
Set up for continuous operation
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Contents
Preface
ix
How to Use This Guide... ix How to Obtain More Information... x How to Obtain Support... xi
Safety
xiii
Safety Conventions Used in This Document... xiv Symbols on Instruments... xv Safety Labels on Instruments... xvi General Instrument Safety... xvii Chemical Safety... xviii Chemical Waste Safety... xx Electrical Safety... xxi Physical Hazard Safety... xxi Laser Safety... xxi Workstation Safety... xxii Safety and Electromagnetic Compatibility (EMC) Standards... xxiii
Chapter 1
Preparing the Instrument
1
Instrument Description... 2 Application Summary Tables... 3 Barcode Readers... 6
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Starting the 3130/3130xl Genetic Analyzer System... 7 Data Collection Software... 9 Preparing the Instrument... 11 Preparing Buffer and Filling Reservoirs... 16
Chapter 2
Performing a Spatial Calibration
21
Spatial Calibration... 22 Creating a Spatial Calibration File... 22 Evaluating a Spatial Calibration File... 23 Examples of Spatial Profiles... 25
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Chapter 3
Performing a Spectral Calibration
27
Spectral Calibration... 28 Preparing the Spectral Calibration Chemistry... 31 Loading Samples... 32 Creating a Spectral Instrument Protocol... 35 Performing a Spectral Calibration... 37 Evaluating the Spectral Calibration Data... 43 Activating a Spectral Calibration... 47 Examples of Passing Sequencing Spectral Calibrations... 49 Examples of Passing Fragment Analysis Spectral Calibrations... 51
Chapter 4
Autoanalysis and Sequencing Analysis Software
53
Sequencing Analysis Software... 54 About Plate Records and Sequencing Analysis... 55 Creating Protocols for Automated Sequencing Analysis... 59 Analysis Protocol for Sequencing Analysis... 62 Results Group for Sequencing Analysis... 70 Filling Out a Sequencing Analysis Plate Record... 77
Chapter 5
Autoanalysis and SeqScape Software
81
SeqScape Software... 82 About Plate Records and Seqscape Software... 83 Creating Protocols for Automated SeqScape Software Analysis... 88 Filling Out a SeqScape Software Plate Record... 101
Chapter 6
Autoanalysis and Fragment Analysis
105
GeneMapper Software... 106 Creating Protocols for Automated Fragment Analysis... 112
Chapter 7
Running the Instrument
127
Preparing Samples and Plate Assemblies... 128 Linking and Unlinking a Plate... 128 Running the Instrument... 130 Controlling the Run... 133 Set Up for Continuous Operation... 134 Working with Data in The Run History View... 145 Viewing Data from a Completed Run in the Data Collection Software... 146
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Creating a GeneMapper Software Plate Record... 123
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About GeneMapper Software Plate Records... 108
Viewing Autoextraction Results... 147 Using Autoanalysis Manager Software... 155 Viewing Analyzed Data... 160
Appendix A Plate Mapping
161
Injection Scheduling... 161 Capillary Array Map... 161 96-Well Plate Mapping... 162 384-Well Plate Mapping... 163
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Index
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Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide
SAMPLE DOCUMENT
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Preface How to Use This Guide Purpose of This Guide
The Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide provides step-by-step instructions for preparing and analyzing a sample. It is designed to help you quickly learn how to use the Applied Biosystems 3130/3130xl Genetic Analyzers.
Audience
This manual is written for principle investigators and laboratory staff who are planning to operate and maintain the Applied Biosystems 3130/3130xl Genetic Analyzers.
Assumptions
This guide assumes you have the following background: • Familiarity with Microsoft® Windows® XP operating system. • Knowledge of general techniques for handling DNA samples and preparing them for electrophoresis. • A general understanding of hard drives, data storage, file transfers, and copying and pasting. If you want to integrate the 3130/3130xl Genetic Analyzers into your existing laboratory data flow system, you need networking experience.
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Text Conventions
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 dropdown 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.
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Preface How to Obtain More Information
Examples of the user attention words appear below: Note: The size of the column affects the run time.
IMPORTANT! To verify your client connection to the database, you need a valid Oracle
user ID and password.
Safety Alert Words
Safety alert words also appear in user documentation. For more information, see “Safety Alert Words” on page xiv.
How to Obtain More Information The following related document is shipped with the system: • Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide (P/N 4352716) - Contains information on maintaining the instrument and computer system, troubleshooting tables to diagnose performance failures and advance reference content. • Applied Biosystems 3130/3130xl Genetic Analyzers Site Preparation Guide (P/N 4352717) - Contains the space, environmental, and electrical requirements to support the 3130/3130xl Genetic Analyzer system. • Applied Biosystems 3730/3730xl DNA Analyzers and Applied Biosystems 3130/3130xl Genetic Analyzers AB Navigator Software Administrator Guide (P/N 4359472) - Contains information and procedures for the administrator maintaining the computer system and software files of the Applied Biosystems 3130/3130xl Genetic Analyzers. • Applied Biosystems 3130/3130xl Genetic Analyzers Quick Reference Card (P/N 4362825) - Contains a flowchart on how to run your samples and instrument, a table of maintenance tasks, and a Data Collection software reference guide. Note: For additional documentation, see “How to Obtain Support” on page xi.
Send Us Your Comments
Applied Biosystems welcomes your comments and suggestions for improving its user documents. You can e-mail your comments to:
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Related Documentation
Preface How to Obtain Support
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
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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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Preface
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How to Obtain Support
Safety
This safety section describes the following: Safety Conventions Used in This Document... xiv Symbols on Instruments... xv Safety Labels on Instruments...xvi General Instrument Safety... xvii Chemical Safety...xviii Chemical Waste Safety... xx Electrical Safety... xxi Physical Hazard Safety...xxi Laser Safety...xxi Workstation Safety... xxii
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Safety and Electromagnetic Compatibility (EMC) Standards... xxiii
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Safety Safety Conventions Used in This Document
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.
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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 xvi).
Safety Symbols on Instruments
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
microtiter 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.
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.
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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.
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Safety Safety Labels on Instruments
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 xvi). 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. 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
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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.
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English
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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.
Safety General Instrument Safety
English
Francais
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.
DANGER Class 3B laser radiation present when open and interlock defeated. Avoid direct exposure to laser beam.
DANGER Class 3B rayonnement laser en cas d’ouverture et d’une neutralisation des dispositifs de sécurité. Eviter toute exposition directe avec le faisceau.
DANGER Class 3B laser radiation when open. Avoid direct exposure to laser beam.
DANGER Class 3B rayonnement laser en cas d’ouverture. Eviter toute exposition directe avec le faisceau.
DANGER Class 2(II) laser radiation present when open and interlock defeated. Do not stare directly into the beam
DANGER de Class 2(II) 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) laser radiation present when open. Do not stare directly into the beam.
DANGER de Class 2(II) rayonnement laser en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
DANGER Class 2(II) LED when open and interlock defeated. Do not stare directly into the beam.
DANGER de Class 2(II) LED en cas d'ouverture et d'une neutralisation des dispositifs de securite. Eviter toute exposition directe avec le faisceau.
DANGER Class 2(II) LED when open. Do not stare directly into the beam.
DANGER de Class 2(II) LED en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
CAUTION Moving parts.
ATTENTION Parties mobiles.
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General Instrument Safety PHYSICAL INJURY HAZARD. Use this product only as specified in this document. Using this instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument.
Moving and Lifting 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.
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Safety Chemical Safety
Moving and Lifting StandAlone Computers and Monitors
Do not attempt to lift or move the computer or the monitor without the assistance of others. Depending on the weight of the computer and/or the monitor, moving them may require two or more people. Things to consider before lifting the computer and/or the monitor: • Make sure that you have a secure, comfortable grip on the computer or the monitor when lifting. • Make sure that the path from where the object is to where it is being moved is clear of obstructions. • Do not lift an object and twist your torso at the same time. • Keep your spine in a good neutral position while lifting with your legs. • Participants should coordinate lift and move intentions with each other before lifting and carrying. • Instead of lifting the object from the packing box, carefully tilt the box on its side and hold it stationary while someone slides the contents out of the box.
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 xviii.
Chemical Safety 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.
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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.
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Chemical Hazard Warning
Safety Chemical Safety
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.
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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 xviii.) • 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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Safety Chemical Waste Safety
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.
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
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disposal limitations may apply.
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Chemical Waste Safety Guidelines