GeneAmp® 5700 Sequence Detection System
Contents
1. 0 0 A GR1173 WARNING For protection against fire hazard replace only with the same type of fuse Figure 2 2 Safety alert symbols left side of instrument Instrument Safety 2 5 CAUTION Refer to manual for lamp replacement WARNING To avoid electrical shock disconnect power cord before servicing Never operate equipment with grounding conductor disconnected WARNING To avoid electrical shock disconnect power cord before servicing CAUTION This unit contains protective circuitry Contact Applied Biosystems service before performing AC line tests y WARNING Grounding circuit continuity is vital for safe operation of equipment Figure 2 3 Safety alert symbols rear of instrument 2 6 Instrument Safety 100 120 220 230 240 VAC 50 60 Hz MAX POWER 250 VA USE 250 V FUSES 5 AMP SB T 5 X 20 MM For protection against fire hazard replace only with same type and rating of fuse gt o o o o o o o o 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 CAUTION Do not restrict air intake or exhaust WARNING To reduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicin2. 3 2 Hazardous Waste tests dace end Hele ein 3 3 OVERVIEW 5 on E ne hee Wave ld Sabb haan Bas aa eae eee 3 3 Material Safety Data Sheets Overview 3 4 General Information rs csi ete A ae EO LS eee eS 3 4 MSDS SECOS is Palas att anse iii 3 4 How to Get Extra Copies of MSDSS 3 4 MSDSs for Applied Biosystems Chemicals 3 4 Acronyms and Abbreviations Used in Waste Profiles and MSDSs A 1 Introduce tint ni pital ook ae ere ty a ee ee UE Ras A 1 Organizations Regulations and Scientific Terminology A 1 Units of Measure Chemicals Site Preparation Before You Start Pre installation Operator Training Performance Verification Ordering Supplies Unpacking Before the instrument is installed the installation site must be prepared so that the instrument can operate correctly and safely Careful attention to the requirements presented here will simplify the installation procedure Training of operators is one of the primary goals of installation Persons who are to be trained to operate the instrument should set aside two uninterrupted days to work with the Applied Biosystems service representative If this is not possible the installation should be rescheduled Calibration of the instrument and verification of performance will be performed by an App
3. 1 6 Site Preparation Items Shipped with This Instrument Summary Hazardous Chemicals Warning Installation Chemical Kit The GeneAmp 5700 Sequence Detection System is shipped with the following GeneAmp 5700 Accessories Box GeneAmp 5700 Sequence Detection System User s Manual Software Installation and Lab Supplies Installation Chemical Kit P N 4303134 GeneAmp 5700 Sequence Detector contains the 5700 Electronics Unit and Optics Assembly 9600 Thermal Cycler only included with complete systems Windows NT compatible PC Do not unpack any cartons related to the instrument itself This will protect you from liability if any damage occurred during shipping IMPORTANT You must unpack the Installation Chemical Kit and store the components as specified in Table 1 1 below WARNING Some chemicals used with Applied Biosystems instruments are hazardous and can cause injury illness or death Always read the appropriate Waste Profiles and MSDSs before interacting with the instrument and chemicals in any way Hazardous Chemical Warnings are prominently displayed on the labels of all hazardous materials Before unpacking the Installation Chemical Kit storing chemicals or interacting with the chemicals and instrument read Chapter 3 Chemical Safety of this manual Chapter 3 contains the Waste Profiles and Material Safety Data Sheets MSDSs that pertain to this instrument Unpack the Installation
4. Applied Biosystems MDS Sciex 1 800 952 4716 1 650 638 6223 Outside North America Region Telephone Dial Fax Dial Africa and the Middle East Africa English Speaking and West Asia Fairlands South Africa 27 11 478 0411 27 11 478 0349 South Africa Johannesburg 27 11 478 0411 27 11 478 0349 Middle Eastern Countries and North Africa Monza Italia 39 0 39 8389 481 39 0 39 8389 493 Eastern Asia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 86 10 64106617 Site Preparation 1 3 1 4 Site Preparation Telephone Fax Region Dial Dial Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2 593 6470 6471 82 2 593 6472 Malaysia Petaling Jaya 60 3 758 8268 60 3 754 9043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 22358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 750 43 0 1 867 35 75 11 Belgium 32 0 2 712 5555 32 0 2 712 5516 Czech Republic and Slovakia Praha 420 2 61 222 164 420 2 61 222 168 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101
5. through the a Access the Applied Biosystems Technical Support Web site at Internet for fax or http www appliedbiosystems com techsupp e mail delivery b Under Resource Libraries click the type of document you want c Enter or select the requested information in the displayed form then click Search d In the displayed search results select a check box for the method of delivery for each document that matches your criteria then click Deliver Selected Documents Now or click the PDF icon for the document to download it immediately e Fill in the information form if you have not previously done so then click Deliver Selected Documents Now to submit your order Note There is a limit of five documents per request for fax delivery but no limit on the number of documents you can order for e mail delivery Site Preparation 1 5 Preinstallation Checklist About this Checklist Use this checklist to ensure that all preparations have been made for installation A service representative will contact you to verify that everything is checked off before the installation date Checklist Check off and enter a date to ensure that all preparations are complete 5700 Preinstallation Checklist Vif Date ready Confirmed Components General Received instrument s and verified that cartons are intact Read this Site Preparation and Safety Guide including MSDSs Verified that instrument s serial number
6. Telephone Dial Fax Dial ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 Biolnformatics includes BioLIMS BioMerge and SQL GT applications 1 800 831 6844 then press 25 1 505 982 7690 Peptide Synthesis 433 and 43X Systems 1 800 831 6844 then press 31 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 then press 32 1 650 638 5981 PCR and Sequence Detection 1 800 762 4001 then press 1 for PCR 2 for the 7700 or 5700 6 for the 6700 or dial 1 800 831 6844 then press 5 1 240 453 4613 Voyager MALDI TOF Biospectrometry and Mariner ESI TOF Mass Spectrometry Workstations 1 800 899 5858 then press 13 1 508 383 7855 Biochromatography BioCAD Workstations and Poros Perfusion Chromatography Products 1 800 899 5858 then press 14 1 508 383 7855 Expedite Nucleic acid Synthesis Systems 1 800 899 5858 then press 15 1 508 383 7855 Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5858 then press 15 1 508 383 7855 PNA Custom and Synthesis 1 800 899 5858 then press 15 1 508 383 7855 FMAT 8100 HTS System and Cytofluor 4000 Fluorescence Plate Reader 1 800 899 5858 then press 16 1 508 383 7855 Chemiluminescence Tropix 1 800 542 2369 U S only or 1 781 271 0045 1 781 275 8581
7. 13 AVG ii do Uy ae une ABR AN ace nee es 1 13 Temperature and Humidity 1 13 Pollution so a He ann aie aden an nn ora E io ee 1 13 is a a ee a EE 1 13 Emission Immunity Statement 0 0 00 cee ee eee ee eee 1 13 Laboratory Ventilation 2 1 13 MED E it E AS A AR RA 1 13 2 Instrument Safety Instrument Safety Overview 2 1 Sale OPTOMA RE SG LE ne Ne er Een 2 1 Us r Attention Words eii aria id Best seein Nine te a 2 1 Instr mentELabeld8 series ea nine eed ete re ae nd ne 2 1 Safety Labels tnt SE nn ae din aire e are Reda D ets 2 1 Signal Words sio A Se ee A een ae 2 1 Labels That May Be Found On Your Instrument 2 2 Safety Alert SYMbO S 2 5 58 led grb a DM ns aoe bates dut ne aaa 2 3 Electrical Symbols sue Ll ct E SSAA RAS Wee densit 2 3 Non electrical Symbols 2 3 Input Output Connections 2 8 ECO gio is cette eer A ben Men nt tbe date dE nd pes 2 8 Chemical Safety IO UCA E A A A AS ere Dios E A 3 1 Please read sn ta ia pas ee eed nia dE E da 3 1 Hazardous Chemicals 0 0 setae a ak ave te Rare todas ou wba Be un ee Pnau 3 2 Oyeryie Wae iss Sette Saat eae oranda eds Dot Sr en ere site Dr 3 2 Handling Hazardous Chemicals
8. this level of heat output For our European customers any product marked with the CE label meets the European requirements for emission and immunity as defined in the EMC Directive 89 336 EEC and the Low Voltage Directive 72 23 EEC This product meets Class A emission limits Laboratory Ventilation Venting This instrument uses chemicals that are hazardous chlorinated organic liquids WARNING Some Applied Biosystems instruments use chemicals that are hazardous Always mix and prepare hazardous materials beneath an operating fume hood Site Preparation 1 13 Instrument Safety Instrument Safety Overview Safe Operation User Attention Words Before operating the instrument read the information in this section concerning hazards and potential hazards Ensure that anyone involved with the operation of the instrument is instructed in both general safety practices for laboratories and specific safety practices for the instrument Four user attention words appear in the text of all documentation for Applied Biosystems products Each word implies a particular level of observation or action that is significant to user safety or proper instrument operation Note Calls attention to useful information IMPORTANT Indicates information that is necessary for proper instrument operation CAUTION Cautions the user that a potentially hazardous situation could occur causing injury to the user or damage to the instrument if this info
9. 101 Hungary Budapest 36 0 1 270 8398 36 0 1 270 8288 Italy Milano 39 0 39 83891 39 0 39 838 9492 Norway Oslo 47 23 12 06 05 47 231205 75 Poland Lithuania Latvia and Estonia 48 22 866 40 10 48 22 866 40 20 Warszawa Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Russia Moskva 7 095 935 8888 7 095 564 8787 South East Europe Zagreb Croatia 385 1 34 91 927 385 1 34 91 840 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 1206 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d lJssel 31 0 180 331400 31 0 180 331409 United Kingdom Warrington Cheshire 44 0 1925 825650 44 0 1925 282502 All other countries not listed 44 0 1925 282481 44 0 1925 282509 Warrington UK Japan Japan Hacchobori Chuo Ku Tokyo 81 3 5566 6100 81 3 5566 6501 Latin America Del A Obregon Mexico 305 670 4350 305 670 4349 To Reach Technical We strongly encourage you to visit our Web site for answers to frequently asked Support Through questions and for more information about our products You can also order technical the Internet documents or an index of available documents and have them faxed or e mailed to you through our site The Applied Biosystems Web site address is http www appliedbiosystems com techs
10. Chemical Kit upon receipt The Installation Chemical Kit is intended to be used during installation to verify instrument performance Store the chemicals and reagents as indicated in the table below Table 1 1 Installation Chemical Kit Components P N 4303134 Storage P N Description Conditions 4303135 SYBR Green DNA Core PCR Reagents 20 C 401970 TaqMan DNA Template Reagents 20 C 4304965 Protocol Ambient Site Preparation 1 7 Items Needed but Not Supplied Resupply The Installation Chemical Kit components are completely consumed during the installation and initial testing of the instrument To ensure an uninterrupted supply of reagents and eliminate the higher transportation costs of rush shipments you should order additional chemicals and supplies in advance Water Equipment and Supplies 1 8 Site Preparation Although the Installation Chemical Kit contains all the reagents necessary for operating the instrument each laboratory must provide its own source of high quality deionized water In addition to the Installation Chemical Kit the following equipment and supplies are needed for operation of the GeneAmp 5700 4 Micro pipettes and PCR compatible pipette tips Wet and dry ice and ice buckets Freezer with a stable temperature of 20 C Additional optical caps and 96 well PCR trays for post installation work Data backup system floppy disks external hard drives ZIP driv
11. GeneAmp 5700 Sequence Detection System Site Preparation and Safety Guide NS Applied KS Biosystems Copyright 2000 Applied Biosystems For Research Use Only Not for use in diagnostic procedures ABI PRISM and GeneAmp are registered trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries All other trademarks are the sole property of their respective owners Contents 1 Site Preparation Before You Staff ess ts Geld e dort be nn ati dune EE 1 1 Pre mstalati n isene ennenen A a Re 1 1 Operator Tr dde 1 1 Performance Verification 1 1 Ordering Suppltes s apa iee a he tlle re Ad A as 1 1 Unpacking ses eek a ea nee ee da ee Bw ee Ea a ee 1 1 T chnical SUpport sus get aden aie gd eee ae nor Reflet 1 2 Contacting Technical Support 1 2 To Contact Technical Support by E Mail 1 2 Hours for Telephone Technical Support 1 2 To Contact Technical Support by Telephone or Fax 1 2 To Reach Technical Support Through the Internet 1 5 To Obtain Documents on Demand 1 5 Preinstallation Checklists ici bea med batia ew ead ee 1 6 About this Checklist ios ae been Se ok 1 6 Checklist tia A A A esate A ee a 1 6 Items Shipped with This Instru
12. Mtr 4 methoxy 2 3 6 trimethyl benzene sulfonyl Mts mesitylene 2 sulfonyl NMI 1 Methylimidazole NMP N Methylpyrrolidone N methyl 2 pyrrolidone OBt ethyl ester OMe methyl ester PAM resin phenylacetamidomethyl resin PEG polyethylene glycol RV reaction vessel SSPS solid phase peptide synthesis T thymine TETD tetraethylthiuram disulfide TFA trifluoroacetic acid TFMSA trifluoromethane sulfonic acid THF tetrahydrofuran Tos 4 toluenesulfonyl tosyl Tri trityl U uracil Z benzyloxcarbonyl A 4 Acronyms and Abbreviations Worldwide Sales Offices Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For international office locations please call our local office or refer to our web site at www appliedbiosystems com Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 www appliedbiosystems com AS Applied D Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 12 2000 Part Number 4304501E
13. SA Canada 120 10 50 60 Hz 1 Europe pre 1992 220 10 50 60 Hz 1 EC 230 10 50 60 Hz 1 UK pre 1992 240 6 10 50 60 Hz 1 Australia 240 6 10 50 60 Hz 1 Certain types of electrical noise are greatly exaggerated by poor or improper electrical ground connections To prevent these problems it is very important to have a dedicated line and ground between the instrument and building main electrical service The instrument is shipped with electrical cords that are compatible to standard electrical outlets as found in the United States Japan Australia Europe EC and the United Kingdom pre EC Line voltage must be within 10 or as specified above High or low voltages may have adverse effects on the electronic components of the instrument In areas where the supplied power is subject to fluctuations exceeding these limits a power line regulator may be required Short duration high voltage spikes often cause random failures in microprocessor controlled instrumentation These spikes can be caused by other devices using the same power source refrigerators air conditioners and centrifuges or by outside influences such as lightning A dedicated line and ground between the instrument and building main electrical service are necessary to prevent such problems If your environment contains devices that are electrically noisy or you are in an area with frequent electrical storms a line conditioner wit
14. Weight Instrument 17 cm 52 cm 30 5 cm 9 2 kg ida 6 5 in 20 5 in 12 in 20 2 lbs Thermal Cycler 52 cm 61 cm 30 5 cm 40 5 kg GeneAmp 20 in 24 in 12 in 90 Ibs 9600 Electronics Unit 11 5 cm 33 cm 15cm 3 2 kg 4 5 in 13 in 6 in 7 lbs Computer 41 cm 41 cm 52 cm 20 kg incl monitor 20 in 20 in 20 in 44 Ibs The 5700 must be located within 1 8 m 6 ft of the electrical outlets The instrument requires a laboratory bench or sturdy table of correct dimensions to accommodate the system The instrument must be accessible to the installer on all four sides A clearance of 15 cm 6 in is needed at the rear of the instrument to provide adequate ventilation Additional clearance is required for servicing Do not block access to the rear of the instrument Figure 1 1 Typical laboratory layout for the GeneAmp 5700 Sequence Detection System Electrical Requirements Power Grounding Power Cords Voltage Quality Voltage Spikes The electrical supply 4 electrical outlets should have a dedicated 2 0 kVA power line and ground or a 2 0 kVA power line with a line conditioner or uninterruptible power supply UPS The electrical receptacle must be located within 1 8 m 6 ft of the instrument rear panel The following table specifies the electrical operating range for various parts of the world Location Volts AC Frequency Japan 100 10 50 60 Hz 1 U
15. cted to another instrument s signal ground reference This is not a protected ground terminal This symbol indicates that this is a protective grounding terminal that must be connected to earth ground before any other electrical connections are made to the instrument A terminal marked with this symbol either receives or delivers alternating current or voltage A terminal marked with this symbol can receive or supply an alternating and a direct current or voltage CAUTION This symbol indicates the presence of high voltage and warns the user to proceed with caution gt u reO CAUTION This symbol alerts you to consult the manual for further information and to proceed with caution Non electrical The following is an illustrated glossary of all non electrical safety alert symbols found Symbols on Applied Biosystems instruments CAUTION This symbol illustrates a heater hazard Proceed with caution when working around these areas to avoid being burned by hot components gt gt This symbol indicates that a laser is present inside the instrument Instrument Safety 2 3 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 personnel Figure 2 1 Safety alert symbols front view of instrument 2 4 Instrument Safety
16. e fuses are user replaceable See page 8 18 of the 9600 User s Manual for more information about fuses and fuse replacement procedures Instrument Safety 2 9 Chemical Safety Introduction Please read This chapter contains detailed information for this instrument about Y Hazardous chemicals used if any Hazardous waste produced and how to handle Where appropriate detailed Waste Profiles and Material Safety Data Sheets MSDSs are provided to ensure correct and safe operation of the instrument Applied Biosystems assumes that all operations in your laboratory will be conducted in accordance with safety practices detailed in Waste Profiles and MSDSs and with any applicable laws and regulations Chemical Safety 3 1 Hazardous Chemicals Overview This instrument uses chemicals that are hazardous chlorinated organic liquids Handling Hazardous Chemicals 3 2 Chemical Safety WARNING Hazardous chemicals can cause injury illness or death Handle all chemicals as potentially hazardous Chemicals are classified as hazardous when they are physically hazardous or if they may cause health hazards upon acute or chronic exposure 4 Physically hazardous chemicals are materials that are flammable combustible compressed gasses explosives oxidizers organic peroxides pyrophoric reactive or unstable or water reactive Chemicals that may cause health hazards are materials that are carcinogens toxic or highly toxic
17. eparate cable CCD card PCB installed inside of the PC This 15 pin female socket connects to the 5700 sequence detector that is mounted on top of the 9600 Keyboard and Mouse sockets These are round din connectors Monitor Port This 7 pin female socket connects to the PC s monitor Voltage Select Switch This 2 position switch is located next to the power cord s receptacle The voltage sensing PC s monitor also has a power cord receptacle Back of GeneAmp 5700 Electronics Unit Control Port This 15 pin female socket is connected to IEEE1284 port on the PC Electrical Output Port This large plastic 8 pin female socket connects to the GeneAmp 5700 optics assembly that is mounted on top of the 9600 Fuse Holder The fuse is located next to the power cord receptacle 2 8 Instrument Safety Back of 5700 Sequence Detector There are two 2 cables that originate from the back of the 5700 optics One cable connects to the 5700 electronics units 8 pin connector and the other cable connects to the 15 pin female socket on the PC s CCD card PCB installed inside of the PC Left Side of 9600 RS 232 Port This 25 pin male socket connects to the PC s 1 serial port 7 pin male socket THe PC s 2 serial port is not used Fuse Holder The fuses are located next to the power cord receptacle There are Two 15 amp Slo Blow fuses for 100 120 Vac instruments One 8 amp Slo Blow fuses for 220 240 Vac instruments Note Th
18. es etc Laboratory Safety Onsite Your laboratory has specific safety practices and policies designed to protect Representative laboratory personnel from the potential hazards both obvious and hidden that are present We request that a representative from your laboratory be in the vicinity and available to our engineer at all times while he or she is on site Required Safety The following safety equipment should be available Equipment Fire extinguisher Halon Eye wash Safety shower Eye and hand protection Adequate ventilation First aid equipment Spill clean up equipment o Protection from sources of radiation lasers radioisotopes contaminated equipment radioactive wastes etc that may be present in the area where our engineer will be working Site Preparation 1 9 Laboratory Space Required Dimensions and Weight Location of Instrument Clearance Typical Laboratory Layout 1 10 Site Preparation The GeneAmp 5700 Sequence Detection System requires at least 0 56 m 20 in vertical clearance and 1 22 m 4 ft horizontal bench space The vertical clearance will accommodate the computer when its monitor is placed on top This vertical clearance will also accommodate the sequence detector and thermal cycler which mount on top of each other The horizontal space will accommodate the computer thermal cycler optics and a small electronics unit Component Width Depth Height
19. fund is a federal las administered by EPA DFG MAK Federal Republic of Germany s Maximum Contamination Value in the workplace similar to PEL in the USA DOT United States Department of Transportation regulates transportation of hazardous material USA EPA United States Environmental Protection Agency regulates use disposal or emission of hazardous material USA IDLH Immediate Danger to Life and Health LCio Lowest published lethal concentration LCs Lethal concentration in air that kills 50 of a specified population LD5o Lethal dose that kills 50 of a specified population LEL Lower Explosion Limit MSHA Mine Safety and Health Administration recommends respirators NFPA National Fire Protection Association publishes recommended regulations for local or state governments in the United States Hazardous rating system developed by this Association Acronyms and Abbreviations A 1 Table A 1 Acronyms and Abbreviations continued Term Explanation NIOSH National Institute of Occupational Safety and Health USA recommends exposure levels and respirators oc Open cup testing for flash point OSHA Occupational Safety and Health Administration USA sets chemical exposure levels PEL Permissible Exposure limit The federal OSHA limit usually expressed as TWA for an 8 hour work shift PPM Parts Per Million Prop 65 A California Law requiring warnings for chemicals t
20. g to Applied Biosystems qualified service personnel WARNING Disconnect supply cord before opening A Grounding circuit continuity is vital for safe operation of equipment Never operate equipment with grounding conductor disconnected Figure 2 4 Safety alert symbols electronics unit Instrument Safety 2 7 Input Output Connections Locations The exact locations of the input output connections on the GeneAmp 5700 Sequence Detection System are shown in Figure 2 5 The input output connections are labeled on the instrument 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 LTD 9000000000 0000 of JO 4 S 900000000000000 of Jo 000000000000000 S 000000000000000 O 000000000000000 SS 000000000000000 P opio Edo O Edo 000 E o Figure 2 5 Input output connections Back of PC IOIOI 1 Serial Port 7 pin male socket connects to the 9600 s serial port IOIOI 2 Serial Port This 7 pin socket is not used Y IEEE 1284 Auxiliary Parallel Port This 25 pin female socket connects to the GeneAmp 5700 s electronics unit The electronics unit is also connected to the GeneAmp 5700 optics by a s
21. h a recommended capacity of 2 0 kVA will enhance the reliability of your system This may be lower depending on the conditioner or power supply design Site Preparation 1 11 Power Outages The instrument has been designed to recover from short periods of power outage loss and continue operation provided that the line voltage does not become excessively noisy before the outage If increased protection during a power outage is desired you may want to install an uninterruptible power supply UPS We recommend a capacity of 2 0 kVA The UPS will involve a higher cost than a line conditioner 1 12 Site Preparation Laboratory Environmental Requirements Altitude Temperature and Humidity Pollution Heat Emission Immunity Statement CE This instrument is for indoor use only and for altitudes not exceeding 2 000 meters 6 500 ft above sea level The laboratory temperature should be maintained between 15 30 C 59 85 F The instrument can tolerate up to 80 relative humidity Avoid placing the instrument adjacent to heaters or cooling ducts The installation category overvoltage category for this instrument is II and it is classified as portable equipment The instrument has a pollution degree rating of 2 and may be installed in an environment that has non conductive pollutants only The thermal output of the instrument is 5000 Btu h 1 500 W Consult your facilities department regarding ventilation requirements for
22. hat are known to the state to be carcinogenic or cause reproductive harm RCRA Resource Conservation and Recovery Act RTECS Registry of Toxic Effects of Chemical Substances SARA Superfund Amendments and Reauthorization Act a federal act administered by EPA SCBA Self Contained Breathing Apparatus STCC Standard Transportation Commodity Code STEL Short Term Exposure Level published by ACGIH Lowest published toxic concentration TLV Threshold Limit Value The ACGIH recommended TWA usually for an 8 hour work shift TWA Time Weighted Average UEL Upper Explosive Limit uorU Unknown UN United Nations This designation identifies hazardous chemicals in the process of world wide transportation Units of Measure Table A 2 lists abbreviations for common units of measure Table A 2 Abbreviations for Common Units of Measure Abbrev Unit of Measure number C degrees Celsius sF degrees Fahrenheit uL microliter um micron umol micromole AUFS absorbency units full scale ft foot i d inside diameter in inch L liter m meter A 2 Acronyms and Abbreviations Table A 2 Abbreviations for Common Units of Measure continued Abbrev Unit of Measure mg milligram mL milliliter mm millimeter o d outside diameter P N Applied Biosystems part number ps
23. i pounds per square inch sec second V volt Chemicals Table A 3 lists abbreviations for common chemicals Table A 3 Abbreviation for Common Chemicals Abbrev Definition A adenine AA amino acid 1Ac acetyl Acl acetylimidazole Acm acetamidomethyl Ac O acetic anhydride ACN acetonitrile ACT activator vessel BHA resin benzhydrylamine resin t Boc tert butyloxycarbonyl Bzl benzyl Br Z 2 bromobenzyloxcarbonyl t Bu tert butyl C cytosine CHO formyl CH Bzl 4 methylbenzyl CH 0Bz 4 methoxybenzyl CI Z 2 chlorobenzyloxycarbonyl CPG Controlled Pore Glass DCA dichloroacetic acid DCC dicyclohexylcarbodiimide DCM dichloromethane DCU dicyclohexylurea DIEA diisopropylethylamine DMAP 4 dimethylaminopyridine DMF dimethylformamide DMSO dimethylsulfoxide DNA deoxyribonucleic acid Acronyms and Abbreviations A 3 Table A 3 Abbreviation for Common Chemicals continued Abbrev Definition Dnp 2 4 dinitrophenyl Et ethyl EtOH ethanol Fmoc 9 fluorenylmethyloxycarbonyl G guanine HBTU 2 1 H benzotriazol 1 yl 1 1 3 3 tetramethyl uronium hexafluorophosphate HLP high loaded polystyrene HMP resin p hydroxymethylphenoxymethyl polystyrene resin HOAc acetic acid mBHA resin 4 methylbenzhydrylamine resin MeOH methanol Mob 4 methoxybenzyl
24. ion contre les risques d incendie remplacer uniquement par un fusible de m me type et de m me courant nominal CAUTION HOT Attention Surface chaude DANGER High voltage Danger Haut Voltage 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 Biosystemsr qualified service personnel Avertissement Pour r duire la chance du choc lectrique ne retirez pas les couvertures qui exigent l acc s d outil Aucune pi ce utile d ulitisateur n est int rieur R f rez l entretien au personnel de service de Applied Biosystems DANGER Laser radiation when open and interlock defeated Avoid direct exposure to beam Danger Rayonnement de Laser si ouvert et couplage a d fait Evitez l exposition directe au faisceau CAUTION Moving parts Attention Pi ces mobiles Safety Alert Symbols Electrical Symbols The following chart is an illustrated glossary of all electrical symbols that are used on Applied Biosystems instruments Whenever such symbols appear on instruments please observe appropriate safety procedures This symbol indicates the on position of the main power switch This symbol indicates the off position of the main power switch This symbol indicates the on off position of a push push main power switch This symbol indicates that a terminal may be conne
25. les d chets avant de manipuler ou d eliminer WARNING Risk of electric shock Disconnect power cord from supply before replacing fuses or removing power supply module from instrument Avertissement Risque de choc lectrique D lectrique D brancher le cordon d alimentation avant de remplacer les fusibles ou de retirer le block d alimentation de l instrument WARNING For continued protection against risk of fire replace only with Listed and Certified fuse of the specified type and ratings Avertissement Pour assurer une protection continue contre les risques d incendie remplacer les fusibles uniquement par des fusibles num r s et certifi s du type de courant nominal specifi s WARNING HOT LAMP Avertissement LAMPE CHAUDE WARNING HOT Replace lamp with an Applied Biosystems lamp Composants chauds Remplacer la lampe par une lampe Applied Biosystems WARNING Disconnect supply cord before opening Grounding circuit continuity is vital for safe operation of equipment Never operate equipment with grounding conductor disconnected Avertissement D brancher la corde d approvisionnement avant l ouverture La continuit de circuit au sol est essentiel pour l exploitation s re du mat riel N actionnez jamais le mat riel avec le conducteur debranch WARNING For protection against fire hazard replace only same type and rating of fuse Avertissement Afin d assurer la protect
26. lied Biosystems service representative during the installation Reagents shipped with this instrument will be consumed during the process of setup and verification Be sure to order additional chemicals and other necessary supplies before installation for the ongoing operation of the instrument Do not unpack instruments Inspect instrument cartons and report any damage to your Applied Biosystems service representative For vital information and instructions about unpacking Installation Chemical Kit see Item Shipped with this Product later in this chapter Site Preparation 1 1 Technical Support Contacting Technical You can contact Applied Biosystems for technical support by telephone or fax by Support e mail or through the Internet You can order Applied Biosystems user documents MSDSs certificates of analysis and other related documents 24 hours a day In addition you can download documents in PDF format from the Applied Biosystems Web site please see the section To Obtain Documents on Demand following the telephone information below To Contact Technical Contact technical support by e mail for help in the following product areas Support by E Mail Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing corelab appliedbiosystems com Peptide and DNA Synthesis Biochromatography PerSe
27. ment 1 7 SUMMA a Gada me ee Sevan A A rs evar anette 1 7 Hazardous Chemicals Warning 1 7 Installation Chemical Kit 1 7 Items Needed but Not Supplied 1 8 Resupply resni iaie bs ates de ae tae ead daa ee ee Rees ds 1 8 A tee ee TRE disease nh thats dei 1 8 Equipment and Supplies viii rer idad au lads 1 8 Laboratory Safety moe a Taree eee AE eee RTE da 1 9 Onsite Representative 2588 men iS ie bee tons Eure 1 9 Required Safety Equipment 1 9 Laboratory Space Required 2 1 10 Dimensions and Weight ocios abr get pee bises de 1 10 Location of Instrument 1 10 Clearance uri E ER A A A weg a Oe Ad 1 10 Typical Laboratory Layout 1 10 Electrical Requirements 30 064 A ane der bed 1 11 POWELL ANT En A SE at Re Re 1 11 Grounding ire Bee Rat Gatto T eA Ba G Re ated orne dt ah 1 11 Power Cords 235 fau sie eines aan rie Ghee Weegee ea Dee aa ee 1 11 Voltage Quality 4 oi hentai a edu ee A aes 1 11 iii Voltage SDIKes de eh vee ies 1 11 POWER OULAS S cs Lane nan A le Li te Se Re 1 12 Laboratory Environmental Requirements 1
28. ptive DNA PNA tsupport appliedbiosystems com and Peptide Synthesis systems CytoFluor FMAT Voyager and Mariner Mass Spectrometers Applied Biosystems MDS Sciex api3 support sciex com Chemiluminescence Tropix tropix appliedbiosystems com Hours for Telephone In the United States and Canada technical support is available at the following times Technical Support Product Hours Chemiluminescence 8 30 a m to 5 30 p m Eastern Time Framingham support 8 00 a m to 6 00 p m Eastern Time All Other Products 5 30 a m to 5 00 p m Pacific Time To Contact Technical In North America Support by To contact Applied Biosystems Technical Support use the telephone or fax numbers Telephone or Fax given below To open a service call for other support needs or in case of an emergency dial 1 800 831 6844 and press 1 Product or Telephone Fax Product Area Dial Dial ABI PRISM 3700 DNA Analyzer 1 800 831 6844 1 650 638 5981 then press 8 DNA Synthesis 1 800 831 6844 1 650 638 5981 then press 21 Fluorescent DNA Sequencing 1 800 831 6844 1 650 638 5981 then press 22 Fluorescent Fragment Analysis includes 1 800 831 6844 1 650 638 5981 GeneScan applications then press 23 Integrated Thermal Cyclers ABI PRISM 1 800 831 6844 1 650 638 5981 877 and Catalyst 800 instruments then press 24 1 2 Site Preparation Product or Product Area
29. r chemicals manufactured by Applied Biosystems are available at no extra cost Call your local representative or access the Applied Biosystems World Wide Web site at www appliedbiosystems com techsupport The MSDSs for chemicals manufactured by Applied Biosystems and used with the GeneAmp 5700 Sequence Detection System are packaged with this device The following MSDS is included in this manual 10X SYBR R Green PCR Buffer P N 4305036 Acronyms and Abbreviations Acronyms and Abbreviations Used in Waste Profiles and MSDSs Introduction Organizations Regulations and Scientific Terminology Waste Profiles and MSDSs use acronyms and abbreviations for certain organizations government regulations common scientific terminology units of measurement and chemicals The following tables contain lists of acronyms and abbreviations commonly used in Waste Profiles and MSDSs Table A 1 lists acronyms and abbreviations for organizations government regulations and scientific terminology Table A 1 Acronyms and Abbreviations Term Explanation ACGIH American Conference of Governmental Industrial Hygienists CAS Chemical Abstract Service Reference Number for Specific Pure Chemical cc Closed cup testing of flash point CFR Code of Federal Regulations Regulations published by the United States Government CERCLA Comprehensive Environmental Response Compensation and Liability Act Super
30. reproductive toxins irritants corrosives sensitizers heptagons nephrotoxins agents that act on the hematopoietic systems and agents that damage the lungs skin eyes or mucous membranes Important requirements for handling hazardous chemicals include 4 4 Read all applicable MSDSs before handling hazardous chemicals When replacing reagents always install the new bottle on the instrument Do not top off old bottles Some chemicals reduce the integrity of glass bottles and repeated use beyond six weeks may result in the bottle fracturing when it is pressurized during operation Provide secondary containment for all reagent bottles Do not store chemicals in direct sunlight or heat on or off the instrument Hazardous Waste Overview This instrument uses chemicals that are hazardous chlorinated organic liquids WARNING Waste produced by this instrument is potentially hazardous and can cause injury illness or death Dispose of the contents of the waste tray and waste bottle in accordance with all applicable health and environmental laws and regulations Ensure that the waste container is correctly installed Always handle hazardous materials beneath a fume hood that is connected in accordance with all installation requirements During transfer ensure that the waste container is tightly sealed with the waste cap provided Read all applicable Material Safety Data Sheets before handling or disposing of hazardo
31. rmation is ignored WARNING Warns the user that serious physical injury or death to the user or other persons could result if these precautions are not taken Instrument Labeling Safety Labels Signal Words Safety labels are located on the instrument Each label consists of a Signal Word panel and a Message panel A Safety Alert Symbol indicates a potential personal safety hazard lf multiple hazards exist the signal word corresponding to the greatest hazard is used CAUTION indicates a potentially hazardous situation that could result in minor or moderate injury to the user or damage to the instrument WARNING indicates a potentially hazardous situation that could result in death or serious injury DANGER indicates an imminently hazardous situation that if not avoided will result in death or serious injury most extreme Instrument Safety 2 1 Labels That May Be The following Danger Caution and Warning labels listed in English and French Found On Your below may be found on your instrument Instrument 2 2 Instrument Safety English French CAUTION Hazardous chemicals Read the Material Safety Data Sheets before handling Attention Produits chimiques dangeureux Lire les fiches techniques de s ret de mat riels avant la manipulation des produits CAUTION Hazardous waste Read the Waste Profile before handling or disposal Attention D chets dangeureux Lire les renseignements sur
32. s and system configuration as shown on the packing list are the same as ordered Set aside one uninterrupted day for in lab training during installation Unpacked and stored contents of the Installation Chemical Kit Electrical A dedicated 2 0 kVA power line and ground or a 2 0 kVA power line with a line conditioner or UPS is in place 4 outlets Four 4 standard power outlets are located within 1 8 m 6 ft of the instrument PC Monitor Electronics Unit Thermal Cycler Instrument voltage if specified on the packing list matches the voltage available in the laboratory Laboratory Laboratory bench is of correct dimensions to accommodate the system and is situated so that the instrument is accessible to the installer on all four sides Laboratory safety requirements as specified in this manual have been met Laboratory environmental requirements as specified in this manual have been met Room ventilation accommodates instrument heat output Deionized water is on site Proper waste disposal method for hazardous chemical waste has been established Equipment PCR Laboratory supplies including tube racks wet amp dry ice Freezer with a stable temperature of 20 C Consumable Supplies Additional Applied Biosystems reagent kits Chemically resistant disposable gloves Additional computer supplies a printer is not supplied
33. upp To submit technical questions from North America or Europe Step Action 1 Access the Applied Biosystems Technical Support Web site 2 Under the Troubleshooting heading click Support Request Forms then select the relevant support region for the product area of interest 3 Enter the requested information and your question in the displayed form then click Ask Us RIGHT NOW blue button with yellow text 4 Enter the required information in the next form if you have not already done so then click Ask Us RIGHT NOW You will receive an e mail reply to your question from one of our technical experts within 24 to 48 hours To Obtain Free 24 hour access to Applied Biosystems technical documents including MSDSs Documents on is available by fax or e mail or by download from our Web site Demand To order documents Then by index number a Access the Applied Biosystems Technical Support Web site at http www appliedbiosystems com techsupp b Click the Index link for the document type you want then find the document you want and record the index number c Use the index number when requesting documents following the procedures below by phone for fax a From the U S or Canada call 1 800 487 6809 or delivery from outside the U S and Canada call 1 858 712 0317 b Follow the voice instructions to order the documents you want Note There is a limit of five documents per request
34. us waste Dispose of hazardous waste in accordance with all local state and federal regulations Chemical Safety 3 3 Material Safety Data Sheets Overview General Information MSDS Sections How to Get Extra Copies of MSDSs MSDSs for Applied Biosystems Chemicals 3 4 Chemical Safety Material Safety Data Sheets provide information about physical characteristics health hazards safety precautions first aid spill cleanup and disposal procedures Read the MSDSs before handling reagents or interacting with the instrument For a complete list of acronyms and abbreviations used in MSDSs see Appendix A Each MSDS is divided into 16 sections although not all sections apply to every chemical The names of the 16 sections are listed below Section 1 Chemical Product and Company Identification Section 2 Composition Information on Ingredients Section 4 First Aid Measures Section 5 Fire Fighting Measures Section 6 Accidental Release Measures Section 7 Handling and Storage Section 8 Exposure Controls Personal Protection Section 9 Physical and Chemical Properties Section 10 Stability and Reactivity Section 11 Toxicological Information Section 12 Ecological Information Section 13 Disposal Considerations Section 14 Transport Information Section 15 Regulatory Information Section 16 Other Information Additional copies of MSDSs fo
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