Applied Biosystems GeneAmp PCR System 9600 User Manual Download Page 295

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Summary of Contents for GeneAmp PCR System 9600

Page 1: ...l service in house repair center WE BUY USED EQUIPMENT Sell your excess underutilized and idle used equipment We also offer credit for buy backs and trade ins www artisantg com WeBuyEquipment REMOTE INSPECTION Remotely inspect equipment before purchasing with our interactive website at www instraview com LOOKING FOR MORE INFORMATION Visit us on the web at www artisantg com for more information on ...

Page 2: ...GeneAmp PCR System 9600 User s Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 3: ...tice the PCR process may be obtained by contacting the Director of Licensing at Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 The information contained in this document is subject to change without notice APPLIED BIOSYSTEMS MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A P...

Page 4: ...ause personal injury if precautions are not followed CAUTION A caution indicates an operation that could cause instrument damage if precautions are not followed Note Notes emphasize significant information in a procedure or description Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 5: ... Consulter les documents d accompagnement If there is a hazard of heat or electric shock the following warning symbols will appear on the instrument 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 AVERTISSEMENT Surface chaude This symbol indicates the dange...

Page 6: ...ndicates alternating current Indicates the primary protective grounding terminal Indicates the off position of the main power switch Indicates the on position of the main power switch Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 7: ...access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour réduire le risque de chocs électriques ne pas ouvrir les couvercies si un outil est nécessaire Ne contient aucune pièce pouvant être réparée par l utilisateur Confier le dépannage au personnel qualifié de Applied Biosystems Left Side of Instrument WARNING For protection ...

Page 8: ...o avoid electrical shock disconnect power cord before servicing AVERTISSEMENT Pour éviter les chocs électriques débrancher le cordon d alimentation avant le dépannage CAUTIONThis unit contains protective circuitry Contact Applied Biosystems Service before performing any AC line tests AVERTISSEMENT Cet appareil contient des circuits de protection Vérifier auprès de Applied Biosystems avant d effect...

Page 9: ...ser serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour réduire le risque de chocs électriques ne pas ouvrir les couvercies si un outil est nécessaire Ne contient aucune pièce pouvant être réparée par l utilisateur Confier le dépannage au personnel qualifié de Applied Biosystems Artisan Technology Group Quality Instrumentation Guarantee...

Page 10: ...ype and rating of fuse AVERTISSEMENT Afin d assurer la protection contre les risques d incendie remplacer uniquement par un fusible de même type et de même courant nominal LEFT SIDE Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 11: ...ical shock disconnect power cord before servicing AVERTISSEMENT Pour éviter les chocs électriques débrancher le cordon d alimentation avant le dépannage CAUTIONThis unit contains protective circuitry Contact Applied Biosystems service before performing any AC line tests AVERTISSEMENT Cet appareil contient des circuits de protection Vérifier auprès de Applied Biosystems avant d effectuer des essais...

Page 12: ...ressors may need to be disconnected before a test is performed On completion of the tests it is essential to reconnect the surge components Electromagnetic Compatibility EMC United States FCC This product is classified as a digital device used exclusively as industrial commercial or medical test equipment It is exempt from the technical standards specified in Part 15 of the FCC Rules and Regulatio...

Page 13: ...ee the best temperature uniformity keep the sample block cover closed at all times except when you are loading samples CAUTION To avoid damaging the sample block or heated cover make sure you turn the cover knob completely counterclockwise before you try to move the heated cover either forward or backward The cover knob must be turned completely counterclockwise to lift the heated plate from the s...

Page 14: ...or indoor use CAUTION Do not operate in a Cold Room or a refrigerated area The PCR 9600 operates most efficiently under the following conditions ambient temperature is 15 to 30 C 59 to 86 F ambient relative humidity is 20 to 80 without condensation altitude is in the range 0 to 2000 meters CAUTION This instrument is not designed for operation in an explosive environment Installation Category This ...

Page 15: ...hat has a protective ground connection To ensure satisfactory and safe operation of the instrument it is essential that the protective ground conductor the green yellow lead of the line power cord is connected to true electrical ground Any interruption of the protective ground conductor inside or outside the instrument or disconnection of the protective ground terminal may impair the protection pr...

Page 16: ... do not wait or if the power is restored quickly after a power failure a fuse may blow This does not mean that there is anything wrong with the instrument It is caused by the refrigeration motor stalling because it is unable to start until the pressure bleeds away which takes about five minutes Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 17: ... and Canada technical support is available at the following times Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing Peptide and DNA Synthesis corelab appliedbiosystems com Biochromatography PerSeptive DNA PNA and Peptide Synthesis systems CytoFluor FMAT Voyager and Mariner Mass ...

Page 18: ...ations 1 800 831 6844 then press 23 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 then press 24 1 650 638 5981 ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 BioInformatics 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 68...

Page 19: ...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 Applied Biosystems MDS Sciex 1 800 952 4716 1 650 638 6223 Region Telephone Dial Fax Dial Africa and the Middle East Africa English Speaking and West Asia Fairlands South Africa 2...

Page 20: ...58 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 101 101 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 23 12 05 75 Poland Lithuania Latvia and Estonia Warszawa 48 22 866 40 10 48 22 866 40 20 Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Russia Mosk...

Page 21: ...5566 6507 Latin America Del A Obregon Mexico 305 670 4350 305 670 4349 Region Telephone Dial Fax Dial 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 informati...

Page 22: ... of five documents per request through the Internet for fax or e mail delivery a Access the Applied Biosystems Technical Support Web site at http www appliedbiosystems com techsupp 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 d...

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Page 24: ...and connect it to a printer Chapter 3 Tutorial Customizing a PCR CYCL Program Includes step by step instructions for customizing a CYCL program and starting a trial run Chapter 4 Software Basics Gives you an overview of the GeneAmp PCR System 9600 software and describes programs and methods Chapter 5 Setting Up PCR Programs and Methods Describes how to customize the HOLD CYCL and AUTO programs and...

Page 25: ...hapter 8 Maintenance Describes periodic maintenance procedures Chapter 9 Troubleshooting Describes how to solve common problems and what to do in case of instrument power loss Chapter 10 Specifications Lists and describes instrument specifications Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 26: ...ar in operation to the DNA Thermal Cycler and DNA Thermal Cycler 480 but there are several important differences These differences affect the following areas sample block sample tubes PCR files and programs function keys file storage operation setting hold times Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 27: ...ample surface because the heated cover eliminates condensation in the tubes Sample Tubes The GeneAmp PCR System 9600 uses 0 2 mL MicroAmp Reaction Tubes or 0 2 mL MicroAmp Reaction Tubes with Caps with a 96 position MicroAmp Tray Retainer The GeneAmp PCR System 9600 can also use Thin Walled GeneAmp Reaction Tubes Use of these 0 5 mL tubes requires a Thin Walled GeneAmp Tray which holds 480 tubes S...

Page 28: ...e default value 0 01 for the fastest possible ramp time STEP CYCLE File 4 You cannot program ramp times target temperatures are reached as quickly as possible CYCL Program ramp times and hold times as desired for each setpoint CYCL Use the default value 0 00 for the fastest possible ramp time AUTO SEGMENT EXTENSION THERMO CYCLE or STEP CYCLE with auto segment extension AUTO This program can automa...

Page 29: ...ess FILE Then press ENTER Select UTIL on the main menu Access the Configuration and Diagnostic files Press FILE Then press YES Select UTIL on the main menu Move the cursor to the next display or parameter Press STEP Press STEP Move the cursor to the previous dis play or parameter Press HELP Press BACK Toggle between two run time dis plays Press HELP Press MORE Move the cursor to the next selection...

Page 30: ...is necessary The accuracy of the block temperature can be verified using the Temperature Verification Kit Applied Biosystems Part No N801 0434 for the DNA Thermal Cycler Part No N801 0435 for the GeneAmp PCR System 9600 When the DNA Thermal Cycler is in an idle state you cannot control the block temperature the temperature drifts to ambient On the GeneAmp PCR System 9600 block temperature is contr...

Page 31: ...e before the target temperature while the GeneAmp PCR System 9600 starts counting the hold time when the samples reach a temperature one degree before the target temperature As shown in Figure 1 since the block reaches the target temperature before the samples the programmed hold time on the Thermal Cycler must include enough time for the samples to reach the target temperature A hold time of one ...

Page 32: ...7 Figure 1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 Graphic Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 33: ...required to reach the next target temperature See Table 2 For up ramps determine the change in temperature required to reach the next target temperature then round off this value to the closest value given below Then subtract the number of seconds indicated from the hold time used for the DNA Thermal Cycler The result is the hold time to use for the GeneAmp PCR System 9600 The typically recommende...

Page 34: ...commended hold time is 10 to 15 seconds for annealing Note If methods developed on the GeneAmp PCR System 9600 are to be used on the DNA Thermal Cycler you can use Table 2 to convert the hold times from GeneAmp PCR System 9600 to DNA Thermal Cycler by adding the indicated times instead of subtracting them Table 2 After Down Ramps Converting Hold Times Greater than One Minute DNA Thermal Cycler to ...

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Page 36: ...A Look at the Sample Block 1 3 A Look at the Control Panel 1 4 Instrument Features 1 5 The GeneAmp PCR System 9600 Software 1 5 Chapter 2 Installing the GeneAmp PCR System 9600 2 1 Introduction 2 1 Unpacking 2 2 Parts Supplied 2 2 Supplies Accessories and Replacement Parts 2 3 Power Requirements 2 4 Proper Location 2 5 Temperature Humidity and Environment 2 5 Artisan Technology Group Quality Instr...

Page 37: ...3 2 What is a CYCL Program 3 3 Starting Up the Instrument 3 5 Getting to the CYCL Program 3 6 A Look at the CYCL Program 3 9 Customizing the CYCL Program 3 14 Defining the Number of Setpoints 3 14 Defining Values for Setpoint 1 3 15 Defining Values for Setpoint 2 3 17 Defining Values for Setpoint 3 3 17 Specifying the Number of Cycles 3 18 Storing Your CYCL Program 3 20 Starting a Trial Run 3 22 L...

Page 38: ...he AUTO Program 4 12 PCR Methods 4 14 Chapter 5 Setting Up PCR Programs and Methods 5 1 Introduction 5 1 Setting Hold Times on the GeneAmp PCR System 9600 5 2 Editing Keys 5 8 Creating and Editing Programs 5 9 Creating a Program 5 10 Storing the Program 5 11 Editing a Program 5 13 Printing a Program 5 16 Creating and Editing Methods 5 17 Creating a Method 5 18 Storing the Method 5 21 Editing a Met...

Page 39: ...pter 6 Running PCR Samples 6 1 Introduction 6 1 Loading Samples 6 2 Using the 96 Position Sample Tray with MicroAmp Reaction Tubes 6 2 Placing the Sample Tray in the Block 6 5 Using the Cap Installing Tool 6 8 Removing the Sample Tray from the Block 6 8 Removing Samples from the Tray 6 9 Specifying a Program or Method 6 10 Create a new program or method 6 10 Edit an existing program or method 6 10...

Page 40: ...ng Programs by their User Number USER 7 10 Printing a Directory of Your Programs PRINT 7 13 The Configuration Function CONFIG 7 16 Editing the Configuration Parameters 7 16 Setting the Time and Date 7 18 Turning the Run Time Printer Mode and Run Time Beeper On or Off 7 20 Changing the Pause Time Out Limit 7 22 Changing the Allowed Setpoint Error 7 23 Entering an Idle State Setpoint Value 7 25 Chan...

Page 41: ...ng the System Performance Test 7 54 Running the Verify Calibration Test 7 56 The Delete Function DEL 7 57 Deleting Programs by Program Number 7 57 Deleting Programs by User Number 7 59 Deleting All Unprotected Programs 7 61 Chapter 8 Maintenance 8 1 Introduction 8 1 Cleaning the Sample Wells 8 2 Cleaning the Heated Cover 8 3 Temperature Calibration Verification Test 8 4 Equipment Required 8 4 Veri...

Page 42: ...1 Power Requirements 10 2 Control Panel 10 2 Display 10 2 Keypad 10 2 Indicator Lights 10 2 Sample Temperature Range 10 3 Sample Temperature Accuracy 10 3 Displayed Sample Temperature 10 3 Sample Block Temperature Uniformity 10 3 Sample Temperature Overshoot 10 3 Ramp Time Repeatability 10 4 Sample Heating and Cooling Rate 10 4 Printer Interface 10 5 Temperature Calibration 10 5 Index Artisan Tech...

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Page 44: ... 5 Figure 3 4 Moving through the CYCL program displays 3 13 Figure 3 5 Sliding the heated cover forward for a trial run 3 23 Figure 4 1 Keypad 4 2 Figure 4 2 Access to the major functions of the software 4 5 Figure 4 3 HOLD CYCL AUTO and METH programs 4 7 Figure 4 4 A HOLD program held for an indefinite time 4 9 Figure 4 5 A HOLD program held for a specific time interval 4 9 Figure 4 6 A common CY...

Page 45: ...ecuring the retainer on the tray 6 4 Figure 6 3 Placing the sample tray in the block 6 5 Figure 6 4 Sliding the heated cover forward 6 6 Figure 6 5 Turning the cover knob 6 7 Figure 6 6 Removing samples from the tray 6 9 Figure 6 7 Run Time Keys 6 11 Figure 6 8 An example printout of a CYCL program using the SETPOINT option 6 15 Figure 6 9 Run time displays for a CYCL program 6 17 Figure 6 10 Usin...

Page 46: ...ror messages ERROR and printing records PRINT 7 47 Figure 7 13 Printout of all status and data records ALL of a typical History file 7 49 Figure 8 1 Location of sample wells E1 and D1 8 5 Figure 8 2 Placing the probe assembly into the sample wells 8 6 Figure 8 3 Temperature measurements in the temperature calibration verification test 8 9 Figure 8 4 GeneAmp PCR System 9600 Calibration Label 8 10 F...

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Page 48: ...ble utilizing all of the instrument s features Note The unpacking and setup procedures for the GeneAmp PCR System 9600 are included in Chapter 2 of this manual If your instrument has not been installed by an Applied Biosystems Service Representative you should first refer to the instructions given in Chapter 2 For a summary of the instrument s main features and how to use them refer to the Quick R...

Page 49: ...ting up PCR programs and methods 6 When you are ready to run your own samples refer to Chapter 6 to learn how to load a sample tray and run a PCR program 7 Select other chapters according to your needs Chapter 7 describes the Utilities functions These instrument functions let you display or print programs configure the instrument to your needs review a history of the run perform instrument diagnos...

Page 50: ...w Messages seen on the display and referred to in the text are enclosed in quotation marks For example Pause during run Keys are printed in all capital letters and in bold type For example OPTION The names of the different types of programs stored in the software are often referred to by their abbreviations on the screen display HOLD CYCL and AUTO Select Option 9600 RUN CREATE EDIT UTIL CYCL 26 xx...

Page 51: ...ause personal injury if precautions are not followed CAUTION A caution indicates an operation that could cause instrument damage if precautions are not followed Note Notes emphasize significant information in a procedure or description Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 52: ...1 Introduction This chapter describes the principles of instrument operation the hardware and the software Figure 1 1 The GeneAmp PCR System 9600 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 53: ...ed primers with a DNA polymerase by warming the reaction mixture to an intermediate temperature 72 degrees C The anneal and extend steps can be combined into a single setpoint called two temperature PCR The original DNA segment can be either a small discrete molecule whose sequence is already known or a part of a much larger molecule in a complex mixture such as a chromosome fragment The product o...

Page 54: ...the block When a tray is in place the heated cover is moved forward over the sample block area and exerts an even pressure on all tubes Figure 1 2 Sample block and heated cover There are 17 holes within the block for coolant flow eight of the holes are used for rapid sample block cooling ramp cooling and the remaining nine are for cold biasing the system A Kapton heater beneath the sample block is...

Page 55: ...ts of a 40 character blue fluorescent display three indicator lights that show you when the sample block is heating cooling or hot and the keypad The keypad includes standard numeric keys and eight function keys used for creating storing editing or running PCR cycles Figure 1 3 The control panel Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 56: ...oil free operation The GeneAmp PCR System 9600 Software PCR time and temperature profiles are stored by the GeneAmp PCR System 9600 in programs A program is a set of instructions that specify how the instrument should heat and cool your samples in a PCR cycle There are three types of programs stored in instrument memory abbreviated as the HOLD CYCL and AUTO programs Each program contains a thermal...

Page 57: ... increment or decrement the setpoint time and or temperature a fixed amount every cycle view the current status of your PCR cycle on one of two run time displays review comprehensive run time information in a history of the run run software diagnostics to help you solve common problems configure the instrument for use with an optional printer Artisan Technology Group Quality Instrumentation Guaran...

Page 58: ...pplied Biosystems Service Representative disregard these instructions The following sections are included in this chapter Parts Supplied Power Requirements Proper Location Operating Precautions Printer Setup and Configuration optional Heater and Chiller Tests Configuring the System 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 59: ...ended WARNING Improper lifting can cause painful and sometimes permanent back injury Use proper lifting techniques when lifting or moving the instrument Parts Supplied The following parts are supplied with the GeneAmp PCR System 9600 Item Part No Quantity PCR System Starter Kit Consumable items for instrument operations N801 0538 1 Line Cord Domestic 120V N801 6033 1 Line Cord Continental Europe 2...

Page 60: ...If you are located within the U S call toll free 1 800 327 3002 Monday Friday 8 a m to 8 p m EST Your order will be shipped promptly usually within 24 hours If you are located outside of the U S call your local Applied Biosystems sales office 230 220V Conversion Kit shipped with 230V unit N801 0110 1 100V 50Hz to 60Hz Conversion Kit shipped with 100V unit N801 0111 1 PCR System 9600 Video Domestic...

Page 61: ...nt Part No N801 0003 a conversion kit is required and included Applied Biosystems Part No N801 0111 120 VAC and 100 VAC units are supplied with a three terminal plug One of the terminals is an earth ground To protect yourself against shock hazards the electrical outlet must be a properly wired three terminal outlet conforming to National Electric Code Do not use an adapter to a two terminal outlet...

Page 62: ...a solid to prevent vibration stable level surface that allows free air flow especially around the sides and back Temperature Humidity and Environment Observe the following precautions when locating the instrument in your laboratory Do not place the unit in a location subject to wide temperature fluctuation such as direct sunlight air drafts or heat generating equipment Avoid placing the unit in an...

Page 63: ...ure the printer as described on page 2 12 Installing the 115 VAC Printer The Printer Kit for the 115 VAC GeneAmp PCR System 9600 Part No N801 0313 contains a printer Part No 0942 1015 with both a serial adapter card and a printer cable Part No N801 0421 1 Set the DIP switches on the Epson C82302 serial adapter card as shown in Figure 2 1 2 Install the serial adapter card in the printer as describe...

Page 64: ... must be in the ON LINE position See page 3 3 of the Epson LX 810 User s manual When setting the DIP switches on the serial interface cards remember that the ON setting is the same as the CLOSED setting and the OFF setting is the same as the OPEN setting The correct DIP switch settings on the Epson C82302 serial adapter card are SW1 SW2 1 OFF 1 ON 2 OFF 2 ON 3 OFF 3 OFF 4 OFF 4 OFF 5 OFF 5 OFF 6 O...

Page 65: ...2 8 Figure 2 1 DIP switch Settings on the Epson C82302 serial interface card Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 66: ...ve an LX 810 9600 Baud No Parity 8 data bits 1 stop bit ON SW1 8 1 SW2 4 1 Epson LX 810 Printer Right Side Panel Note When installing the serial interface card in the Epson LX 810 see pages 5 38 to 5 51 in the Epson LX 810 Users Manual Serial Port Instrument Power Cord Connection ON OFF Switch Cable N801 0421 Fuse Holders Epson LX 810 Printer Rear Panel Artisan Technology Group Quality Instrumenta...

Page 67: ...on page 5 45 Once the board has been installed pay special attention to Attaching the Upper Case on page 5 49 of the Epson LX 810 User s Manual 3 Set the DIP switches SW1 and SW2 on the right side panel of the printer to the positions shown in Figure 2 2 4 Connect a local plug to the primary line cord of the adapter 0942 1002 as described in the adapter instruction sheet 0993 8359 and connect the ...

Page 68: ...sition See page 3 3 of the Epson LX 810 User s manual After you have installed and connected the printer you must configure the GeneAmp PCR System 9600 for the printer as described on the following pages Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 69: ...pears under the R in RUN 2 Press the OPTION key three times The cursor moves under UTIL 3 Press ENTER The utilities menu is displayed 4 Press the OPTION key once to move the cursor under CONFIG then press ENTER to select configuration Select Option 9600 RUN CREATE EDIT UTIL Select Option 9600 RUN CREATE EDIT UTIL Select function DIR CONFIG DIAG DEL Artisan Technology Group Quality Instrumentation ...

Page 70: ...eeper on or off When the run time printer mode is on you can print run time data When the run time beeper is on a beeper will sound at the end of each setpoint in a run 8 Press the OPTION key to toggle the OFF on the top line of the display to ON then press ENTER The instrument is now configured for a printer 9 If you don t want to hear a beeper sound at the end of each setpoint press the OPTION k...

Page 71: ...s the clock start sample tube time constants Access the configuration parameters as follows 1 The Utilities menu shown below should be displayed If not access the main menu and select UTIL 2 Press OPTION to move the cursor to CONFIG then press ENTER The first configuration display is shown Refer to the following pages for instructions on editing configuration parameters For more detailed instructi...

Page 72: ...ess the OPTION key to change ON to OFF then press ENTER Press STEP to move to the next display Or press BACK to move to the previous display Pause time out limit xx xx Set the maximum amount of time that a program can pause before it is aborted This pertains only to the keypad pause The default value is 10 minutes Press STEP to move to the next display Or press BACK to move to the previous display...

Page 73: ... is 1 0 degree C We highly recommend that you use the default value for this parameter See Chapter 7 for details Press STEP to move to the next display Or press BACK to move to the previous display Special tube NO This display lets you specify a special type of sample tube when you start a run if you are not using MicroAmp Reaction Tubes or Thin Walled GeneAmp Reaction Tubes The default condition ...

Page 74: ...0 µL There is a time constant default value for sample tubes with a reaction volume of 20 µL that appears on a separate display Press STEP to view this display c To change any of these time constant values press the appropriate numeric keys then press ENTER To move the cursor from one time constant value to the next or to move from the first display to the second press STEP Press BACK to move to t...

Page 75: ...or MicroAmp Reaction Tubes and Thin Walled GeneAmp Reaction Tubes We recommend that you only change these values if instructed to do so by future documentation For more information see pages 7 28 to 7 33 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 76: ... an empty MicroAmp Tray MicroAmp Tray Retainer Set Part No N801 0530 on the sample block then slide the heated cover forward and turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover 1 Access the main menu shown below This display appears a few seconds after you turn on the instrument At any other time you can get to the main menu by pressing the ...

Page 77: ...pears on the display as shown below proceed to the chiller test If Heater Test Failed appears on the display notify an Applied Biosystems Service Engineer 5 Press STOP to go to the next test Test 3 Next you will run the chiller test which is accessible from the first diagnostic display Enter Diag test 1 REVIEW HISTORY FILE Enter Diag test 2 HEATER TEST Heater Test Passed Artisan Technology Group Q...

Page 78: ...cedure on page 2 19 2 To access the chiller test press 3 and press ENTER The following display appears and the test begins The test takes from 3 to 12 minutes to complete If Chiller Test Passed appears on the display as shown below the refrigeration system is operating correctly If Chiller Test Failed appears on the display notify an Applied Biosystems Service Engineer 3 Press STOP to exit the tes...

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Page 80: ...ment and get to the CYCL program use the keypad to view all the displays in the CYCL program customize the CYCL program by entering your own times and temperatures for a PCR profile start a trial run By working through this tutorial you ll become familiar with the basic operation of the system in about 30 minutes You ll see how quick and easy it is to enter times and temperatures for a PCR profile...

Page 81: ...plied Biosystems service representative or according to the supplied instructions in Chapter 2 Installation in this manual 2 Read Chapter 1 in this manual 3 Unwrap one of the MicroAmp Trays supplied with the instrument Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 82: ...our PCR application you can easily customize the program to your needs The CYCL program is a common type of PCR thermal profile Typically it consists of two or three setpoints or incubation temperatures see Figure 3 1 The first setpoint is used for template denaturation or melting The second setpoint is used for primer annealing and the third setpoint is used for primer extension Each cycle may be...

Page 83: ...rature and time values for Setpoint 1 The display in Figure 3 2 shows the default values for Setpoint 1 Defaults are commonly used times temperatures and other values For example the default ramp time is 0 00 minutes This causes the sample to heat or cool to the target temperature as fast as possible You can change the default times and temperatures as necessary to customize the program You will s...

Page 84: ...o the ON position Figure 3 3 Location of power switch A beeper sounds and all three indicator lights on the control panel flash The screen lights up and a series of displays appear Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 85: ...g the STOP key one or two times Note If you press the wrong key in the steps that follow press STOP one or two times to return to the main menu and start again 2 Look for the cursor on the main menu The cursor is the short line that appears under the R in RUN 1 The cursor marks the current selection on the display Select Option 9600 RUN CREATE EDIT UTIL Select Option 9600 RUN CREATE EDIT UTIL Curs...

Page 86: ...he OPTION key to move the cursor from one selection to the next b When the cursor reaches the last selection UTIL press OPTION to move the cursor to the first selection again The OPTION key is used the same way on many different displays Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 87: ...n then you press ENTER to accept it You ll do this again in the next step 6 Press the OPTION key to move the cursor under CYCL This option allows you to create a CYCL program Then press ENTER to accept this selection The first display in the CYCL program appears Select Option 9600 RUN CREATE EDIT UTIL Cursor Create program HOLD CYCL AUTO METH 3 Temperature PCR Artisan Technology Group Quality Inst...

Page 88: ...ogram should still be on your display This display sets the number of setpoints or incubation temperatures in one cycle The cursor marks the default value 3 which specifies three temperature PCR cycling 2 Press STEP This accepts the default value of three set points and moves you to the next display This display sets the ramp time temperature and hold time for Setpoint 1 typically used for templat...

Page 89: ...the default ramp time temperature and hold time for Setpoint 2 The display for Setpoint 3 appears This display sets the ramp time temperature and hold time for Setpoint 3 used for primer extension For a three temperature cycle the third PCR setpoint is commonly 72 degrees C and is held for 30 seconds 5 Press STEP to accept the default ramp time temperature and hold time for Setpoint 3 Setpt 2 Ramp...

Page 90: ...will be repeated The prompt that reads Pause during run is used to automatically interrupt a run in the first or successive cycles This lets you add reagents or add or remove samples then continue the run Total cycles 25 Pause during run NO Setpt 3 Ramp 0 00 72 0C Hold 0 30 Total cycles 25 Pause during run No Back Press To display the previous screen Total cycles 25 Pause during run NO Artisan Tec...

Page 91: ...go through the program again to customize it with new PCR parameters 9 Press STEP to return to the first display You have now viewed the main displays in the standard CYCL program and the default parameters for a common PCR profile Figure 3 4 on the next page summarizes how to use the keypad to move through a program CYCL xx xC RUN STORE PRINT HOME 3 Temperature PCR Artisan Technology Group Qualit...

Page 92: ...3 13 Figure 3 4 Moving through the CYCL program displays Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 93: ...play If it does not press STOP one or two times to return to the main menu Then refer to Getting to the CYCL Program on page 3 6 2 In this display you specify the number of setpoints to be used in the program For example if you wanted to perform two temperature PCR you would press 2 For this tutorial you will set up a three temperature PCR program so just press ENTER to accept the de fault value o...

Page 94: ... time Press ENTER to accept 0 00 minutes The cursor moves to the temperature entry 3 Change the temperature to 96 5 degrees C Press 9 then 6 then 5 If you make a mistake press CE Clear Entry to erase the value then start again When the value is correct press ENTER Note that the temperature is set to the nearest tenth of a degree To enter a whole number such as 94 degrees C you must specify 94 0 pr...

Page 95: ... press ENTER to move the cursor forward again to the hold time 6 For this example we will not change the default hold time Press ENTER to accept 0 30 seconds for the hold time The display for Setpoint 2 appears Setpt 1 Ramp 0 00 96 0C Hold 0 30 Back Press To move the cursor back to the previous parameter Setpt 1 Ramp 0 00 94 0C Hold 0 30 Setpt 2 Ramp 0 00 55 0C Hold 0 30 Artisan Technology Group Q...

Page 96: ...y for Setpoint 3 appears Defining Values for Setpoint 3 1 Use the default ramp time by pressing ENTER 2 Enter 74 5 degrees C for the temperature Press ENTER 3 We will not change the hold time Press STEP to skip over this entry and move to the next display Setpt 2 Ramp 0 00 55 0C Hold 0 30 Setpt 3 Ramp 0 00 72 0C Hold 0 30 Total cycles 25 Pause during run NO Artisan Technology Group Quality Instrum...

Page 97: ...d to change a NO selection to a YES and vice versa The illustration below shows how this function of the OPTION key works a Press the OPTION key once The YES option appears in place of NO b For this example no pause will be specified Press OPTION again to display NO then press ENTER to accept this selection and proceed Total cycles 25 Pause during run NO Option Press To change NO to YES and vice v...

Page 98: ...number yet since it hasn t been stored Store the program following the procedure on the next page This will allow you to run the program you have customized at any time in the future without needing to set it up again O CYCL xx xC RUN STORE PRINT HOME Program Number not yet assigned Program Type CYCL Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 99: ...nt x would be a 1 on the display 3 Press ENTER to store the program under the displayed number The following display appears 4 This display gives you the option of protecting the program under a user identification number More details on this option are given in the next chapter For this example choose NO and press ENTER CYCL xx xC RUN STORE PRINT HOME Store Enter program x Store Protect program N...

Page 100: ...r is available Or by selecting HOME to return to the main menu you could create or edit other programs or link together a series of pro grams in a PCR method Our next step will be to use the stored program for a trial run without loading any samples 6 Press OPTION to move the cursor to HOME then press ENTER The main menu appears Prog x OK to store YES O CYCL 1 xx xC RUN STORE PRINT HOME Assigned P...

Page 101: ...is should be done whenever you move the heated cover to ensure that the heated plate underneath is filly raised 2 Slide the heated cover away from you 3 Locate an empty sample tray and orient it so that the cutout in the lower rim is on the left side Place the tray in the sample block 4 Move the heated cover forward to cover the sample compartment to safeguard against burns No samples are loaded i...

Page 102: ...3 23 Figure 3 5 Sliding the heated cover forward for a trial run Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 103: ...he ENTER key The following display appears 4 This display lets you define the type of sample tube you are using and the reaction volume of that tube Press ENTER to accept the default values displayed Note If the printer has been enabled using the Utilities function a display that reads Select print mode appears Select OFF and press ENTER since a printer is not used in this example Select Option 96...

Page 104: ...ime displays alternately appear during ramps and holds in the run 6 Press the MORE key to display more information about the run A second run time display appears O Ramp to 96 5C xx xC 0 30 Cycle 1 Current cycle Time remaining in current Current sample Setpoint temperature temperature ramp or hold segment O Ramp to 96 5C xx xC 0 22 Cycle 1 Current cycle Time remaining in current Current sample Set...

Page 105: ...e program A display similar to the one shown below appears O Setpt 1 Tot Cyc 30 Hrs left 0 7 Prog 1 Current program Estimated time left in Total cycles in program Current setpoint number program More Press To move between the two run time dis plays O Ramp to 96 5C xx xC 0 30 Cycle 1 Setpt 1 Tot Cyc 30 Hrs left 0 7 Prog 1 CYCL 1 xx xC Abort program YES Artisan Technology Group Quality Instrumentati...

Page 106: ...isplay in the program for two temperature PCR then customize the rest of the program as you like In Chapter 4 you will find a summary of the keypad functions and more information about the software and the main menu Chapter 5 explains how to customize any of the three PCR programs available HOLD CYCL and AUTO and how to link programs together to create a method In Chapter 6 you will find informati...

Page 107: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 108: ...L and AUTO programs and PCR methods Included are the following main sections Reviewing Keypad Basics A Close Look at the Main Menu An Overview of PCR Programs and Methods The HOLD Program CYCL The Cycle Program The AUTO Program PCR Methods 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 109: ...de of the keypad are function keys used to select the thermal cycling parameters and run programs The right side of the keypad is used to specify numeric values for example time and temperatures for an analysis or the number of cycles After you type a numeric value you press the ENTER key Figure 4 1 Keypad Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 110: ...rt and stop an analysis Editing keys are used to move through the different displays and select program options The ENTER key is also considered an editing key After you select an item by marking it with the cursor pressing ENTER accepts your selection Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 111: ...ns on the main menu are described below Select Option 9600 RUN CREATE EDIT UTIL Function When to select RUN Select this option to start PCR thermal cycling on samples using any of the PCR programs that you have stored CREATE Select this option to create a new PCR program EDIT Select this option to make changes to any of the PCR programs you have stored UTIL Select the UTIL Utilities option to see ...

Page 112: ...play for the option you selected For example when you select RUN or EDIT you will be asked to enter the number of a program When you select CREATE you then select the type of program you want to use For UTIL you are asked to select a Utilities function for example a directory or listing of your programs Figure 4 2 Access to the major functions of the software Artisan Technology Group Quality Instr...

Page 113: ...ribed below A HOLD program consists of a single temperature held for a specific time interval or for an extended e g overnight period A CYCL Cycle program comprises a repeated pattern of temperature ramp and hold segments for PCR cycling In an AUTO program a more versatile form of CYCL program the setpoint time and or temperature can be automatically incremented or decremented a fixed amount every...

Page 114: ...n easily access and run them later Up to 150 programs be stored on the GeneAmp PCR System 9600 A program can be a method a series of linked programs or an individual program Both methods and programs are assigned program numbers Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 115: ...HOLD programs A HOLD program would normally be used before or after running a CYCL program For example a high temperature e g 94 degrees C HOLD might be used before cycling and a low temperature e g 4 degrees C HOLD might be used after cycling The clock starts when the sample temperature is within one degree C of the target temperature Artisan Technology Group Quality Instrumentation Guaranteed 88...

Page 116: ...Figure 4 4 A HOLD program held for an indefinite time Figure 4 5 A HOLD program held for a specific time interval Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 117: ...r example the setpoint temperature can be set to 94 degrees C for about 10 to 20 seconds when double strands of DNA are separated into single strands The second setpoint is commonly used for primer annealing For example the setpoint temperature can be lowered to between 45 and 55 degrees C for typically not less than 15 seconds when a unique pair of primers bind or anneal to the start and end poin...

Page 118: ...4 11 Figure 4 6 A common CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 119: ...es in product An AUTO program may also be desirable when it is found that the melting temperature of DNA is increasing as the DNA becomes more concentrated In this instance an AUTO program would be used to incrementally increase the denaturation temperature over a series of cycles Another use of an AUTO program is to incrementally increase the annealing temperature over the first several cycles fo...

Page 120: ...4 13 Figure 4 7 An AUTO program used to increase hold time Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 121: ...gure 4 8 This method starts with a HOLD file used for pre PCR denaturation e g 94 0 degrees C for five minutes This is followed by a CYCL program for three temperature PCR A final HOLD program concludes the run for post PCR storage overnight at 4 0 degrees C for example Figure 4 8 An example of a PCR method Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com...

Page 122: ...p a PCR method in which you specify a sequence of programs for a run For example pre PCR incubations PCR cycling and post PCR incubations can be linked together in a single method You will also learn how to store edit and print the methods you create At the end of this chapter you will find information on the displays found in the HOLD CYCL and AUTO programs 5 Artisan Technology Group Quality Inst...

Page 123: ... time when the block reaches a temperature one degree before the target temperature while the GeneAmp PCR System 9600 starts counting the hold time when the samples reach a temperature one degree before the target temperature As shown in Figure 5 1 since the block reaches the target temperature before the samples the programmed hold time on the DNA Thermal Cycler must include enough time for the s...

Page 124: ...5 3 Figure 5 1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 125: ...rature required to reach the next target temperature See Table 5 2 For up ramps determine the change in temperature required to reach the next target temperature and round this off to the closest value given below Then subtract the number of seconds indicated from the hold time used for the DNA Thermal Cycler This will give you the hold time to use for the GeneAmp PCR System 9600 The typically rec...

Page 126: ... Cycler giving us a new hold time of 35 seconds Figure 5 2 Sample conversion of hold times for up ramps DNA Thermal Cycler to GeneAmp PCR System 9600 Note If methods developed on the GeneAmp PCR System 9600 will be used on the DNA Thermal Cycler you can also use Table 5 1 to convert the hold times Simply add the indicated times instead of subtracting them Artisan Technology Group Quality Instrumen...

Page 127: ...r of seconds to subtract from the DNA Thermal Cycler hold time to arrive at the new hold time The typically recommended hold time is 10 to 15 seconds for annealing Seconds to Subtract from DNA Thermal Cycler Hold Times 1 min Figure 5 3 shows an example of converted hold times Temp Starting Temperature of Ramp C C 35 55 56 75 76 95 10 39 sec 39 sec 40 sec 15 45 sec 47 sec 48 sec 20 49 sec 52 sec 53...

Page 128: ...cler giving us a new hold time of 27 seconds Figure 5 3 Sample conversion of hold times for down ramps DNA Thermal Cycler to GeneAmp PCR System 9600 Note If methods developed on the GeneAmp PCR System 9600 will be used on the DNA Thermal Cycler you can also use Table 5 2 to convert the hold times Simply add the indicated times instead of subtracting them Artisan Technology Group Quality Instrument...

Page 129: ...or to the next parameter or display OPTION Moves the cursor to your selection Changes a YES response to a NO and vice versa STOP Returns you to the last display in a program when pressed once When pressed twice returns you to the main menu CE Clear Entry Clears the numeric entry marked by the cursor ENTER Accepts the selection marked by the cursor Artisan Technology Group Quality Instrumentation G...

Page 130: ...ssigned a program number 3 View the displays in the program and make any changes to the thermal cycling parameters 4 In the last display in the program you can choose to RUN Allows you to run a program that you have customized and stored immediately If you do not store the program first you will have to recreate it if you want to use it later STORE Allows you to save the program you have customize...

Page 131: ...escribed in the tables at the end of this chapter The last display to appear allows you to run store or print the program For example this display appears at the end of a CYCL program 5 In most cases you will want to store the program and assign it a number so that it can be run at any time Use the following procedure to store the program Select Option 9600 RUN CREATE EDIT UTIL Create a program HO...

Page 132: ...der the displayed number OR To use a different number type the number 1 150 then press ENTER The following display appears 3 The above display gives you the option of protecting the file under a user identification number By doing so the file cannot be overwritten or deleted unless the user number is entered Select YES or NO by pressing the OPTION key then press ENTER Store Enter program x Store P...

Page 133: ...f you see a display that reads Prog x OK to overwrite you typed a number in Step 2 that has already been used Press OPTION key to select YES or NO YES stores the new file and erases overwrites the old one NO cancels the action and lets you choose a new number see the beginning of this procedure 4 Press ENTER to store the program Store Enter user Prog x User xxxx OK to store YES Artisan Technology ...

Page 134: ... Access the main menu 2 Press the OPTION key to select EDIT then press ENTER You obtain the following display 3 Type the number of the program you wish to edit then press ENTER The first display for the program or method appears For example if you are editing a CYCL program you will see the display that reads 3 temperature PCR Select Option 9600 RUN CREATE EDIT UTIL Edit Enter program Artisan Tech...

Page 135: ...R The following display appears The next available number x appears at the cursor 6 To store the program you have two options You can create a new copy of the program and save the old one see Step 6a Or you can replace the original program with the new version see Step 6b a Press ENTER to store the program under the next available number the one that appears in the display This will create a new p...

Page 136: ...l program was protected you will need to enter the user identification number that was specified when the program was first created before you can overwrite it The following display will appear Type the correct user number then press ENTER The next display will ask OK to overwrite Select YES and the original program will be overwritten by the new edited version Prog x is protected Enter user _ Art...

Page 137: ... this display while you are in a program press STOP 2 Press the OPTION key twice to select PRINT then press ENTER The program is printed AB GeneAmp PCR System 9600 Ver 2 June 1 1992 10 52 am CYCL Progr Program Parameters 3 Temperature PCR SetPt 1 Ramp 0 00 94 0C Hold 0 30 SetPt 2 Ramp 0 00 55 0C Hold 0 30 SetPT 3 Ramp 0 00 72 0C Hold 0 30 Total cycles 25 Pause during run NO Figure 5 5 Example of a...

Page 138: ...have already stored and assigned a number 3 Link together a series of programs 4 In the next display you can choose to RUN Allows you to run the method immediately If you do not store the method first you will have to recreate it if you want to use it later STORE Allows you to save the method before running it Once you have stored a method it may be run at any time PRINT Select this option to prin...

Page 139: ...NTER You obtain the following display 3 Press the OPTION key to select METH then press ENTER The following display appears 4 Type the program numbers of the programs you want linked After you type each number press ENTER For example to link programs 1 3 and 5 your display would look like this Select Option 9600 RUN CREATE EDIT UTIL Create program HOLD CYCL AUTO METH Link progs _ Link progs 1 3 5 A...

Page 140: ...in a method the following display appears This display lets you link up to ten additional programs in the method Note You cannot link a method 6 Type the program numbers of the programs you want linked After you type each number press ENTER 7 Press STEP to move to the next display This display allows you to run store or print the method In most cases you will want to store the method so that it ca...

Page 141: ...cases you will want to store the method and assign it a number so that it can be run at any time Use the following procedure to store the method METH xx xC RUN STORE PRINT HOME Program Type Method Program Number not yet assigned Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 142: ...umber type the number 1 150 then press ENTER The following display appears 3 The above display gives you the option of protecting the file under a user identification number By doing so the file cannot be overwritten or deleted unless the user number is entered Select YES or NO by pressing the OPTION key then press ENTER If you select YES the following display will appear Store Enter program x Sto...

Page 143: ...reads Prog x OK to overwrite you typed a number in Step 2 that has already been used Press OPTION key to select YES or NO YES stores the new file and erases overwrites the old one NO cancels the action and lets you choose a new number see the beginning of this procedure 4 Press ENTER to store the method Store Enter user Prog x User xxxx OK to store YES Artisan Technology Group Quality Instrumentat...

Page 144: ...Press the OPTION key to select EDIT then press ENTER You obtain the following display 3 Type the number of the method you wish to edit then press ENTER The following display appears 4 If desired edit the sequence of linked programs Select Option 9600 RUN CREATE EDIT UTIL Edit Enter program _ Link progs _ Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 145: ...on see Step 6b a Press ENTER to store the method under the next available number the one that appears in the display This will create a new method The original method that you edited will still be available under its original number Once you press ENTER the next display will ask you if you want to protect the program If you choose to do so you will be asked to enter a user identification number b ...

Page 146: ...tten by the new edited version Printing a Method If the instrument is configured for a printer you can obtain two kinds of printouts for a method For more information on configuring a printer see Chapter 7 Utilities 1 You can print a method when the following display is shown 2 Press the OPTION key twice to select PRINT then press ENTER The following display is shown Prog x is protected Enter user...

Page 147: ...R System 9600 Ver 2 June 1 1992 10 55 am METH Program HOLD Program l CYCL Program 2 HOLD Program 3 Figure 5 6 Example of a method printout using METHOD If you selected the PROGRAM DATA option you will obtain printouts for each program that is specified in the method Figure 5 7 shows an example of a printout using the PROGRAM DATA option Artisan Technology Group Quality Instrumentation Guaranteed 8...

Page 148: ...s 3 Temperature PCR SetPt l Ramp 0 00 94 0C Hold 0 30 SetPt 2 Ramp 0 00 55 0C Hold 0 30 SetPt 3 Ramp 0 00 72 0C Hold 0 30 Total cycles 25 Pause during run NO HOLD Program 3 Program Parameters Hold at 4 0C Hold FOREVER Beep while Hold NO Figure 5 7 Example of a method printout using PROGRAM DATA Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 149: ...then press ENTER The following display appears 3 If you do not wish to store any changes you have made to the program press ENTER to accept the YES response This returns you to the main menu If you change your mind and do not want to leave the program press OPTION to change YES to NO then press ENTER This returns you to the display shown in Step 1 above Then press STEP to display the beginning of ...

Page 150: ...display appears 2 Instead of selecting HOME on this display you can immediately return to the main menu by pressing STOP again However any changes you have made to a program will be lost CYCL xx xC RUN STORE PRINT HOME Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 151: ...r on the top line Then press ENTER Note If the program type you entered is different from the type previously listed this will be indicated on the display For example if you entered the number of a Hold program in the above display HOLD would appear before the program number 3 Once you enter the new program number you can run store or print the program OR view or edit it Press STEP to get to the b...

Page 152: ...nite period These two basic types of programs are shown in Figures 4 4 and 4 5 The Displays in a HOLD Program Figure 5 8 shows the main displays that make up a HOLD program These displays are described on the following pages Figure 5 8 The series of displays in a HOLD program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 153: ...can accept this value by pressing ENTER or use the numeric keys to change the value then press ENTER Remember that the hold time clock starts within one degree C of the target temperature You can specify whether or not you want a beeper to sound during the hold segment Press the OPTION key to change NO on the display to YES and vice versa When the desired response is displayed press ENTER The last...

Page 154: ...mperature The pattern can be repeated up to 99 times Typically there are two or three setpoints in a CYCL program A complete cycle typically requires less than two to four minutes The Displays in a CYCL Program Figure 5 9 shows the main displays that make up a CYCL program Figure 5 9 The main displays in a three temperature CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 8...

Page 155: ...ure The default value is 94 0 degrees C Ramp time the time taken to change from one temperature to another The default value 0 minutes 0 seconds causes the sample to heat or cool to the first setpoint as fast as possible Hold time the length of time the samples will be maintained at the specified temperature The default value is 30 seconds Note If you previously used the DNA Thermal Cycler note th...

Page 156: ...en press ENTER For example to specify fifteen seconds press 1 5 then press ENTER Setpoint 2 in a typical cycle program is used for primer annealing This display sets the ramp time target temperature and hold time for the second setpoint Setpt 2 For a three temperature PCR the default temperature is 55 degrees C For a two temperature PCR the default is 68 degrees C The other default values are show...

Page 157: ...h more than four setpoints is 0 0 degrees A CYCL program call have up to nine setpoints Specifies the number of times the complete cycle will be repeated Type the number of cycles 1 99 then press ENTER This display also allows you to program a pause after a setpoint and cycle that you will specify in subsequent displays A pause would be required for example to add a reagent A pause may also be use...

Page 158: ...ycle after the specified setpoint Press the number of the desired cycle then press ENTER Next you specify how often the pause should occur The default value will be the same value as the total cycles in the program This indicates that the instrument will pause only once during the run To pause more frequently change the default For example to pause every cycle you would press 1 To pause every othe...

Page 159: ...t yet been stored and assigned a number It also displays the calculated sample temperature The options in this display allow you to run store or print the program or return to the main menu CYCL xx xC RUN STORE PRINT HOME Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 160: ...ncrement or decrement the setpoint times and temperatures a fixed amount every cycle The Displays in an AUTO Program Figure 5 10 The main displays in a three temperature AUTO program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 161: ... default value is 94 0 degrees C Hold time the length of time the samples will be maintained at the specified temperature The default value is 30 seconds Note If you previously used the DNA Thermal Cycler note that you will be using shorter hold times for the GeneAmp PCR System 9600 Refer to page 5 2 for more information You can accept any of the default values for Setpoint 1 by pressing the ENTER...

Page 162: ...is display appears if you have elected to change the time and temperature by selecting the YES response in the previous display In this display you specify the values by which the setpoint temperature and hold time will be increased or decreased in successive cycles Use the following steps to enter these values 1 Press the OPTION key to change the down arrow before the temperature value to an up a...

Page 163: ...ich the hold time will increase or decrease or accept the default increment 0 00 which indicates that the hold time will not change Use the numeric keys to enter the time then press ENTER These two displays are used to set the temperature and hold time for the second setpoint Setpt 2 and change the time and temperature values in successive cycles if desired For a three temperature PCR the default ...

Page 164: ...s the number of times the complete cycle will be repeated Type the number of cycles 1 99 then press ENTER This display also allows you to program a pause after a setpoint and cycle that you will specify in subsequent displays A pause would be required for example to add a reagent A pause may also be used to add or remove sample tubes during a run Press the OPTION key to change the NO response defa...

Page 165: ...ycle after the specified setpoint Press the number of the desired cycle then press ENTER Next you specify how often the pause should occur The default value will be the same value as the total cycles in the program This indicates that the instrument will pause only once during the run To pause more frequently change the default For example to pause every cycle you would press 1 To pause every othe...

Page 166: ...t yet been stored and assigned a number It also displays the calculated sample temperature The options in this display allow you to run store or print the program or return to the main menu AUTO xx xC RUN STORE PRINT HOME Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 167: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 168: ...ram or Method Starting a Run Note After you turn on the instrument wait 10 minutes before you run your samples WARNING Never run the instrument without a sample tray in place You will crush the sample tubes and may lose your sample MicroAmp Reaction Tubes have thin and fragile walls To avoid damaging one of these sample tubes do not pinch the conical bottom and always handle the tube at the top 6 ...

Page 169: ...ck 2 Place the MicroAmp Tray onto the base so that the well numbered A1 is located at the upper left corner of the tray The cutout in the outside rim of the tray will then be located on the left side of the tray This orients the tray for the proper fit into the sample block 3 Place MicroAmp Reaction Tubes in the tray Note that the wells in the tray are labeled left to right from 1 through 12 and A...

Page 170: ...6 3 Figure 6 1 Setting up the 96 position sample tray Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 171: ... 6 1 The retainer and the tray are keyed so the retainer can fit only one way If you use only a few sample tubes the retainer is not necessary 5 Pipette the PCR reaction mixture into the sample tubes 6 Cap your sample tubes Depending on how many samples you load you can use individual MicroAmp Caps or you can cut a strip of caps to cover one row of tubes See Using the Cap Installing Tool on page 6...

Page 172: ... block The receptacle in the tray labeled A1 will then be in the upper left hand corner of the block Once the tray is placed in the block be sure that the rim of the tray engages with the channel around the block Figure 6 3 Placing the sample tray in the block CAUTION Do not place the MicroAmp Base in the sample block 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www ...

Page 173: ...clockwise which fully raises the platen before you attempt to slide the heated cover forward Then slide the cover forward Figure 6 4 Sliding the heated cover forward 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 174: ...on the knob lines up with the white mark on the cover indicating the full clockwise position This lowers the platen onto the tray Figure 6 5 Turning the cover knob 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 175: ...end of the tool works best with single rows of eight or 12 caps 4 Use the other end of the tool to press a single cap into a sample tube Using moderate force press the cap down into the tube 5 Verify that all the caps are firmly seated in the sample tubes If necessary use the tool again Removing the Sample Tray from the Block The following procedure describes how to remove the sample tray from the...

Page 176: ...sample caps 2 Remove the tray from the base 3 Grasp one end of the tray with one hand and with your other hand press in the front and back tabs on the retainer see Figure 6 6 Then push up and remove the retainer 4 Remove the sample tubes Figure 6 6 Removing samples from the tray Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 177: ...tore it then run it at any time Or select CREATE on the main menu then choose the method option METH to link together a series of programs You can then immediately run the method or store it then run it at any time Edit an existing program or method Select the EDIT option on the main menu to modify one of the programs or methods that you have stored Once you have edited the file you can immediatel...

Page 178: ...function of each key is described below RUN Starts or restarts a sample run MORE Displays more information about run time parameters PAUSE Interrupts a run so you can add a reagent to your samples or add or remove samples STOP Aborts a run Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 179: ... instructions 2 With the cursor positioned under RUN press ENTER The following display appears 3 Select the desired program by pressing the appropriate numeric keys then ENTER The following display appears This display lets you select the type of sample tube you are using and enter the reaction volume for that tube The default tube type is the MicroAmp Reaction Tube as indicated on the display by ...

Page 180: ...wice will change the displayed tube type to OTHER Select this option if you are using tubes other than MicroAmp Reaction or Thin Walled GeneAmp Reaction Tubes 6 To change the reaction volume press the appropriate numeric keys CAUTION Do not press ENTER until the displayed tube type and the displayed reaction volume are both set correctly Note The next time you run this program the tube type and re...

Page 181: ...he heated cover is closed and tightened down After a few seconds the run starts Select print mode OFF CYCLE SETPOINT OFF Disables data output to the printer for this run CYCLE Prints a message that reads Complete after each cycle SETPOINT Prints actual and programmed time and temperature data for each ramp and hold segment during cycling See Figure 6 8 for an example Setpoint printout of a Cycle p...

Page 182: ...T option WARNING During a sample run keep the heated cover pulled forward and tightened down at all times This will guard against burns and guarantee the best temperature uniformity Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 183: ...he sample temperature Cooling when lit or flashing indicates that ramp cooling is active Note Both of the above lights will be lit simultaneously when the sample is being held at a subambient temperature Hot when lit indicates that the sample temperature is at least 50 degrees C The next section describes the displays that appear on the screen during a run Artisan Technology Group Quality Instrume...

Page 184: ... 9 Figure 6 9 Run time displays for a CYCL program Once a CYCL or AUTO run has started press the MORE key to view a second run time display see Figure 6 10 This run time display includes further information about the run Ramp to 94 0C xx xC 0 00 Cycle 1 Current cycle counts up cycles during a run Setpoint temperature Time remaining Current sample temperature Hold at 94 0C xx xC 0 12 Cycle 1 Curren...

Page 185: ...rst run time display The MORE key toggles between the two run time displays Press To move between the two run time displays More Setpt 1 Tot Cyc 30 Hrs left 0 5 Prog 1 Ramp to 94 0C xx xC 0 30 Cycle 1 Setpt 1 Tot Cyc 25 Hrs left 1 2 Prog 26 Program Current setpoint Estimatedtimeleftin program Total cycles in program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www arti...

Page 186: ...e first run time display Figure 6 12 Run time displays for a HOLD program Hold at 95 0C xx xC 4 30 Prog 1 Current program Programmed target temperature Time remaining Current sample temperature Hrs left 0 2 Prog 1 Press To move between the two run time displays More Current program Time remaining Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 187: ... areas may be hotter than 100 degrees C 1 Press the PAUSE key The instrument beeps and a display similar to the one shown below appears This display occurs in a CYCL program 2 Press RUN to resume the run from where you left off Stopping a Run 1 To abort a run at any time press the STOP key The following appears on the second line of the display 2 If you want to abort the run press ENTER to accept ...

Page 188: ...f you change your mind and do not want to abort the run press the OPTION key to change YES to NO then press ENTER OR Press the RUN key The run resumes 4 To run the program from the beginning select the RUN option CYCL 26 Abort xx xC RUN STORE PRINT HOME Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 189: ...rds list the status messages received during the run such as Method Complete or various error messages Data Records contain records of target temperatures ramp and hold times and other run data To obtain a History file use Diagnostic Test 1 To access this diagnostic test select UTIL on the main menu then select DIAG to use the diagnostic tests Refer to Chapter 7 Utilities for instructions on how t...

Page 190: ...or general instrument operating parameters see page 7 16 review the history of the most recent instrument run and perform heater chiller system performance and calibration verification tests to check instrument integrity see page 7 35 delete individual programs by program number or user number or delete all programs see page 7 57 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88...

Page 191: ...AG DEL DIR Select this function to display or print a listing of your programs by program number type or user number CONFIG Select this function to configure and set default values for general instrument operating parameters DIAG Select this function to review the most recent instrument run and to perform diagnostic tests to verify instrument integrity DEL Select this function to delete individual...

Page 192: ...ROG TYPE USER PRINT Configuration EDIT PRINT Delete PROGRAM USER ALL Enter Diag Test 1 REVIEW History file The Directory function lets you display or print programs by their program number their type or their user number The Delete function lets you delete individual programs by their program number and user number or delete all programs The Configuration function lets you configure and set defaul...

Page 193: ... lets you list your programs by their program number on a series of displays starting with the first program number that you enter To list your programs by their program number 1 Select DIR on the Utilities menu as described on page 7 3 The Directory display appears 2 Press ENTER to select PROG The first display that you see prompts you to enter a program number Directory PROG TYPE USER PRINT Dire...

Page 194: ...display In our example Program 1 is a Hold program 5 Press STEP to view the next display which will list Program 2 In our example Program 2 is a CYCL program 6 Press BACK to view the previous program in the list 7 When you reach the last display in the list press STOP to return to the first Directory display Figure 7 2 on the next page shows an example of a complete list of programs HOLD 1 CYCL 2 ...

Page 195: ... 3 Step to move to the previous display to move forward to the next display Step Back Step Press to return to the first display Press Press to return to the first display Press to return to the first display Press Back Stop Stop Stop Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 196: ...to TYPE then press ENTER The following display appears 3 Press OPTION to move the cursor to the program type for which you want to obtain a listing then press ENTER For example to see a listing of all your HOLD programs press ENTER when the cursor is under the HOLD selection You will see a series of displays that list all your HOLD programs beginning with the first HOLD program Directory PROG TYPE...

Page 197: ...am is HOLD 26 5 Press BACK each time you want to view the previous program in the list 6 You can press STOP at any time to return to the display in which you selected the program type Figure 7 3 on the next page shows an example of a list of programs grouped by program type HOLD 14 HOLD 26 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 198: ...display to move forward to the next display Step Press Press Directory HOLD CYCL AUTO METH to return to the first display Press to return to the first display Press to return to the first display Press Stop Stop Step Back Back Step Stop Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 199: ...y their user number 1 Select DIR on the Utilities menu as described on page 7 3 The Directory display appears 2 Press OPTION twice to move the cursor to USER then press ENTER The first display that you see prompts you to enter a user number 3 Type the user number of the programs you want to list then press ENTER In our example we entered user 7777 Each of the next displays will list a program stor...

Page 200: ...LD program 5 is listed 6 Press BACK to view the previous program in the list 7 You can press STOP at any time to return to the display in which you entered the user number Figure 7 4 on the next page shows an example of a complete list of programs grouped by user number CYCL 6 User 7777 HOLD 5 User 7777 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 201: ...e forward to the next display Step Press Press Directory Enter user 7777 to return to the first display Press to return to the first display Press to return to the first display Press Stop Stop Step Back Back Step Stop User 7777 User 7777 User 7777 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 202: ...splay appears 2 Press OPTION three times to move the cursor to PRINT then press ENTER The following display appears 3 Press the OPTION key to move the cursor to the kind of directory you want to print Program Program Type or User then press ENTER One of the following displays appear prompting you to enter a program select a program type or enter a user Directory PROG TYPE USER PRINT Directory Prin...

Page 203: ...HOLD programs will be printed If the above display is shown type the user of the programs for which you want to print a directory then press ENTER All your programs stored with that user will be printed 4 As your directory is printed the following display appears 5 When printing is complete the first Print display appears Press STOP to the return to the Directory display Directory Print Enter prog...

Page 204: ...hows all the displays in the PRINT selection of the Directory function Figure 7 5 The PRINT selection of the Directory function Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 205: ...ation Parameters There are eleven configuration parameters that you can edit These parameters appear on nine different displays To move forward through the displays press STEP To move backward through the displays press BACK Press STOP at any time to return you to the first Configuration display Press STOP again to return to the Utilities menu Figure 7 6 on the next page shows the displays for the...

Page 206: ... Enter Press to display the first configuration parameter returns you to the Configuration display Stop Start clock within x xC of setpoint moves you to the previous dis play or parameter moves you forward to the next display Step Back Special tube NO Set MICRO tube time constants NO Set THIN tube time constants NO Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artis...

Page 207: ...y appears The cursor appears under the entry field for hours HH on the display shown above 3 To set the time press the appropriate numeric keys for the hours and minutes and press ENTER The display will automatically place a colon to separate the hours from the minutes The cursor will move to the entry field for months MM on the display shown above Configuration EDIT PRINT Time HH MM Date MM DD YY...

Page 208: ...nd press ENTER The display will automatically separate the month day and year 5 Press STEP to display the next configuration parameter or press STOP to return to the first Configuration display Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 209: ... on a beeper will sound at the end of each segment in a run To turn these parameters on or off 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears 2 Press ENTER then press STEP The following display appears 3 The default condition of the run time printer mode is off To turn the run time printer mode on press OPTION OFF changes to ON then press ENTER Configu...

Page 210: ...changes to OFF then press ENTER 5 Press STEP to display the next configuration parameter or press BACK to display the previous configuration parameter Press STOP to return to the first Configuration display Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 211: ...s STEP twice The following display appears The default value of ten minutes and zero seconds 10 00 appears on this display The acceptable range for the pause time out limit is 0 to 99 59 minutes 3 To change the pause time out limit press the appropriate numeric keys then press ENTER The display will automatically place the colon for you Note For practical purposes the pause time out should be at l...

Page 212: ...wed setpoint error value 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears 2 Press ENTER then press STEP three times The following display appears The default value of 2 0 degrees C appears on this display 3 To change the allowed setpoint error press the appropriate numeric keys then press ENTER The display will automatically place the decimal point for y...

Page 213: ...xt configuration parameter or press BACK to display the previous configuration parameter Press STOP to return to the first Configuration display Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 214: ...n parameter 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears 2 Press ENTER then press STEP four times The following display appears 3 To change the idle state setpoint press the appropriate numeric keys then press ENTER For your safety set the idling temperature close to room temperature 4 Press STEP to display the next configuration parameter or press B...

Page 215: ... Figure 7 7 Diagram of a 1 degree C temperature interval The default value for the temperature interval is 1 degree C The Configuration function lets you change this value CAUTION Always check this parameter before you start a run To change the temperature interval for the setpoint clock 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Sample Temperature...

Page 216: ...ase the temperature interval from 1 0 degree C the clock will start closer to the setpoint temperature Note To maintain portability of PCR programs we highly recommend that you use the default value of 1 0 degree C The hold time decreases as the temperature interval for the setpoint clock decreases Change this parameter only for specific experiments 4 Press STEP to display the next configuration p...

Page 217: ... press STEP six times The following display appears This display lets you specify a special type of sample tube when you start a run if you are not using MicroAmp Reaction Tubes or Thin Walled GeneAmp Reaction Tubes The default condition of this parameter is no special tube type as indicated on the display by NO 3 If you accept the default condition you will be able to select one of two standard s...

Page 218: ...d one for sample tubes with a reaction volume of 50 µL There is a time constant default value for sample tubes with a reaction volume of 20 µL that appears on a separate display Press STEP to view this display 6 To change any of these time constant values press the appropriate numeric keys then press ENTER To move the cursor from one time constant value to the next press ENTER To move from the fir...

Page 219: ...stant value for MicroAmp Reaction Tubes 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears 2 Press ENTER then press STEP until the following display appears 3 The default condition of this parameter is no Press the OPTION key NO on the display will change to DEFAULTS 4 Press the OPTION key again DEFAULTS will change to MODIFY Pressing the OPTION key again ...

Page 220: ...µL that appears on a separate display Press STEP to view this display 6 To change any of these time constant values press the appropriate numeric keys then press ENTER To move the cursor from one time constant value to the next press ENTER To move from the first display to the second press STEP To move from the second time constant display to the first press the BACK key 7 Press STOP to return to ...

Page 221: ... 3 The default condition of this parameter is no Press OPTION to change NO to DEFAULTS 4 Press OPTION again to change DEFAULTS to MODIFY Press OPTION again to change MODIFY back to NO 5 Press ENTER If your instrument has software version 1 05 or higher the following display appears If your instrument has software version 1 04 or lower the following display appears Configuration EDIT PRINT Set THIN...

Page 222: ... or higher press STEP to view the following display If your instrument has software version 1 04 or lower press STEP to view the following display 6 To change any of these time constant values press the appropriate numeric keys then press ENTER To move from the first display to the second press STEP To move from the second time constant display to the first press the BACK key If your instrument ha...

Page 223: ...action Tubes Printing the Configuration Parameters The PRINT selection of the Configuration function lets you print all of the configuration parameters To print the parameters 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears 2 Press OPTION to move the cursor to PRINT then press ENTER As the configuration parameters are printed the following display appea...

Page 224: ...ng system test the overall performance of your instrument verify that your instrument is still calibrated Each of the diagnostic tests are numbered 1 through 5 and each test appears on a separate display The diagnostic tests and their corresponding numbers are TEST TEST Review History File 1 Heater Test 2 Chiller Test 3 System Performance Test 4 Verify Calibration 5 Artisan Technology Group Qualit...

Page 225: ... Utilities menu as described on page 7 3 The following display appears 2 Press the numeric key that corresponds to the Diagnostic test you want to run 1 2 3 4 or 5 then press ENTER The display for that test appears To select a diagnostic test by using the STEP or BACK keys 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears Enter Diag Test 1 REVIEW HISTORY FI...

Page 226: ...splays for the five diagnostic tests The following sections describe each diagnostic test in detail Step Stop Press Enter Diag Test 1 REVIEW HISTORY FILE Enter Diag Test 2 HEATER TEST Back Enter Diag Test 3 CHILLER TEST Enter Diag Test 4 SYSTEM PERFORMANCE anytime to return to the Utilities menu Press Press to move to the next display to move to the previous display Enter Diag Test 5 VERIFY CALIBR...

Page 227: ...status messages such as Run Complete or Method Complete data records which display all pertinent numerical data about the run such as temperature and time The History file can contain up to 500 records If a run produces more than 500 records the earliest records are overwritten The previously stored contents of a History file are automatically cleared at the start of a new run When you review the ...

Page 228: ...at an error occurred during the run A status record displays the following information type of program HOLD CYCL AUTO or METH program number or question marks if no program number was assigned method number if the run contained linked programs status record number date on which the run was started completed or aborted time at which the run was started completed or aborted sample tube type sample t...

Page 229: ... hold clock starts and will always be the third record Start mm dd yy hh mm This message shows the date and time the run began and will always be the fourth record End mm dd yy hh mm This message shows the date and time the run ended Meth Complete This message will always appear at the end of a successful method run Sensor Error This message will appear if the sample block temperature was read inc...

Page 230: ...ilure occurred during the run It shows how long the power was off Abort mm dd yy hh mm This message will appear if you pressed the STOP key during the run It shows the time and date the run was aborted Pause Timeout hh mm The pause timeout limit was exceeded during the run Fatal Setpoint Error The sample block did not reach its setpoint in a reasonable period of time Pause xx xx at xx xC The run f...

Page 231: ...nt number except in HOLD programs total setpoint time ramp and hold times error message if an error occurred If the segment was successfully completed the data record will also display type of program H for HOLD C for CYCL A for AUTO or M for METH program number or question marks if no program number was assigned method number if any If an error occurred during the run the data record will display...

Page 232: ...d of time Prog Error This message will appear if when you ran an AUTO program either time became a negative number or the temperature went out of the range of 0 1 to 99 9 C Temp Error This message will appear if at the end of a segment the set point temperature drifted a previously entered amount See Changing the Allowed Setpoint Error in this chapter Artisan Technology Group Quality Instrumentati...

Page 233: ...t number If an error had occurred at this point in the run an error message would also have appeared on this display Displaying the History file To select Diagnostic Test 1 and display the History file 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears 2 Press ENTER to select Diagnostic Test 1 The following display appears Enter Diag Test 1 REVIEW HISTORY FI...

Page 234: ...llowed by either the STEP key or the BACK key a For example to skip forward three records type 3 STEP b To skip backward three records type 3 BACK Figures 7 11 and 7 12 on the next two pages show all the possible displays in an example History file A different example History file is shown in the printout in Figure 7 13 ALL view all the records in the History file beginning with the most recent re...

Page 235: ... to move to the next display to return to the first dis play C 2 25 2C 8 Cyc 2 Setpt 2 0 10 C 2 26 0C 9 Cyc 3 Setpt 1 0 05 The most recent record is displayed first Stop Status Record Data Record Press Press Press Back to move to the previous display C 2 29 8C 7 Cyc 2 Setpt 1 0 10 C 2 25 2C 6 Cyc 1 Setpt 2 0 10 CYCL 2 4 Start 12 21 90 14 45 CYCL 2 3 Clk starts w in 1 0C CYCL 2 1 Tube type MICRO Ar...

Page 236: ... Enter Diag Test 1 REVIEW HISTORY FILE History 10 recs ALL STAT ERROR PRINT Enter Enter History Print ALL STAT ERRORS Enter Press Stop Enter Select this option to print only those data record with error messages Status Message Select this option to print only status records Select this option to print all status and data records to return to the first display CYCL 2 10 Abort 12 21 90 14 47 Artisan...

Page 237: ... press ENTER The following display appears The menu items in this display give you the following choices Select ALL to print all status and data records in the History file Select STAT to print only the status records Select ERRORS to print only those data records that contain error messages Enter Diag Test 1 REVIEW HISTORY FILE History 10 recs ALL STAT ERROR PRINT PRINT HISTORY ALL STAT ERRORS Ar...

Page 238: ...ay appears Figure 7 13 shows a History file printout of all status and data records ALL for a CYCL program Figure 7 13 Printout of all status and data records ALL of a typical History file History Print printing Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 239: ...No N801 0530 on the sample block then slide the heated cover forward and turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover To run the Heater Test 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears 2 Select Diagnostic Test 2 by pressing 2 then pressing ENTER or by pressing the STEP key The following displ...

Page 240: ...oint the following screen appears This display will show Passed if the test was successful If the test was not successful the display will show Failed If this should occur contact an Applied Biosystems Service Engineer 4 Press STOP to return to the first Diagnostic display Heater Test Blk xx x going to 35C Heater Test Passed Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE...

Page 241: ... forward and turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover To run the Chiller Test 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears 2 Select Diagnostic Test 3 by pressing 3 then pressing ENTER or by pressing the STEP key twice The following display appears 3 Press ENTER to start the test Enter Diag...

Page 242: ...drives the sample block cold the temperature is monitored for a specific amount of time and the cooling rate is calculated The following display appears This display will show Passed if the test was successful If the test was not successful the display will show Failed If this should occur contact an Applied Biosystems Service Engineer 4 Press STOP to return to the first Diagnostic display Chiller...

Page 243: ...ut 30 to 40 minutes to complete At the end of the test the system will report the results of the tests with either a pass warning or fail message If any of the tests fail record the results or print them out and contact an Applied Biosystems Service Engineer To run the System Performance Test 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears 2 Select Diagno...

Page 244: ...press ENTER A list of the test results will be printed 6 Review the test results with an Applied Biosystems Service Engineer The Service Engineer will use the results to identify the instrument problem 7 Press STOP to return to the first Diagnostic display System Performance VIEW RUN PRINT VIEW Select this option to view the last test results on a series of displays Use the STEP key to move forwar...

Page 245: ...l calibrated To run this test you will need the Temperature Verification System for the GeneAmp PCR System 9600 Applied Biosystems Part No N801 0435 Refer to Chapter 8 Maintenance for complete instructions on how to verify you instrument s calibration Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 246: ...es if a program is linked in a method that program cannot be deleted until the method is first deleted Deleting Programs by Program Number To delete an individual program by specifying its program number 1 Select DEL on the Utilities menu as described on page 7 3 The following display appears 2 With the cursor positioned under PROGRAM press ENTER Delete PROGRAM USER ALL Artisan Technology Group Qu...

Page 247: ...gram you want to delete then press ENTER You can delete any program or method Note A program cannot be deleted if it is linked in a method or if the program is protected unless the correct user number is entered 4 Press the STOP key at any time to return to the first Delete display Delete Enter program xxx Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 248: ... 3 Press the numeric keys that correspond to the user number of the programs you want to delete then press ENTER If a program is linked in a method it cannot be deleted The following display appears if there is a program that is linked in a method 4 Press the STEP key to scroll through the list of linked programs Delete PROGRAM USER ALL Delete Enter user xxxx Progs linked in meth STEP to list prog...

Page 249: ... The number xxx on the bottom line represents the method number in which the program is linked 5 If you want to delete all the unlinked programs under the given user number press ENTER The following display appears 6 Press ENTER to delete the files Can t delete file xxx Linked in method xxx User xxxx Delete all progs YES Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www...

Page 250: ...g display appears 2 Press the OPTION key twice to move the cursor to ALL then press ENTER The following display appears If you change your mind press the OPTION key to change YES to NO then press the STOP key to return to the first Delete display 3 Press ENTER All unprotected programs will be deleted Delete PROGRAM USER ALL Delete every unprotected prog YES Artisan Technology Group Quality Instrum...

Page 251: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 252: ...d Biosystems Service Representative WARNING Do not remove the instrument cover There are no components inside the GeneAmp PCR System 9600 that you can safely service yourself If you suspect a problem contact an Applied Biosystems Service Representative 8 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 253: ...gree HOLD program to bring the sample block to room temperature then turn off the instrument for 15 minutes 2 Remove the sample tray from the block and set aside 3 Use a cotton swab soaked in isopropanol and clean the sample wells thoroughly Make certain that the isopropanol has evaporated completely before reloading the sample tray If the sample wells become contaminated clean the wells thoroughl...

Page 254: ... 3 of the way towards the back of its range 3 Note that there are notches in the cover rail and taking advantage of the notches lift the cover straight up and set it down on its side on the instrument cover Do not pull the heated cover away from the instrument 4 Soak a clean cloth with isopropanol and gently wipe the bottom of the cover 5 Remove any remaining isopropanol from the cover and replace...

Page 255: ...tton swabs Light mineral oil Probe tray Verifying the Temperature Calibration Perform the procedure as described in the following steps We recommend that you perform this procedure immediately after you turn on the instrument Note Refer to the Instructions included with your Temperature Verification System for a detailed description on operating the digital thermometer 1 If the heated cover is in ...

Page 256: ...of two cones one of which measures the temperature of the sample well The wire is attached to the cone that does not measure the temperature of the sample well This cone is a dummy probe 4 Place the probe assembly into wells D1 and E1 so that the dummy probe sits in D1 Thread the probe wire through the notch in the probe tray see Figure 8 2 Make sure the probe is connected to the digital thermomet...

Page 257: ...k on the cover 6 Turn on the digital thermometer by moving the ON OFF RANGE switch to the 200 position 7 Turn on the GeneAmp PCR System 9600 The main menu appears 8 Press the OPTION key three times to move the cursor to UTIL then press ENTER The utilities menu appears Select Option 9600 RUN CREATE EDIT UTIL Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com...

Page 258: ...he heated cover Cvr xxC and sample block Blk xx xC When the temperature of the heated cover is within ten degrees of the sample block temperature the following display appears This displays shows the current sample block temperature Blk 40 0C and a clock which counts up from zero in minutes and seconds Time MM SS Select function DIR CONFIG DIAG DEL Enter Diag Test 1 REVIEW HISTORY FILE Going to 40...

Page 259: ...shows the current temperatures of the block cover Cvr xxC and the sample block Blk xx xC When the temperature of the block cover is within ten degrees of the sample block temperature the following display appears This displays shows the current sample block temperature Blk 95 0C and a clock which counts up from zero in minutes and seconds Time MM SS Record Temperature Time MM SS Blk 40 0C Going to...

Page 260: ... 5 and ENTER to return to the Verify Calibration Diagnostic test Figure 8 3 shows when you should take the two measurements Figure 8 3 Temperature measurements in the temperature calibration verification test Record Temperature Time MM SS Blk 95 0C 95 40 Temp C Time 0 3 0 3 Clock starts Measure well E1 T 40 Clock starts Measure well E1 T 95 Artisan Technology Group Quality Instrumentation Guarante...

Page 261: ...abel Note If you have more than one GeneAmp PCR System 9600 in your laboratory make sure that the serial number on the calibration label matches the serial number on the instrument you are testing 1 Use the following formula to calculate the average block temperature at the 95 degree hold Block Average at 95 C T 95 High Offset PASTE THE CALIBRATION LABEL HERE Artisan Technology Group Quality Instr...

Page 262: ... average block temperature at the 40 degree C hold Block Average at 40 C T 40 Low Offset If the block average is more than 0 75 degree C above or below 40 degrees C your GeneAmp PCR System 9600 needs to be recalibrated For example If the measured temperature of well E1 was 39 9 C and the Low Offset printed on your calibration label is 0 1 then you would use the following formula for computing the ...

Page 263: ...swabs This completes the test The calibration has now been verified If your instrument needs to be recalibrated contact an Applied Biosystems Service Representative Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 264: ...e block rows A C E and H with mineral oil using a cotton swab 3 Place the probe tray on the sample block with the notch facing the front of the instrument The RTD probe assembly consists of two cones one of which measures the temperature of the sample well The wire is attached to the cone that does not measure the temperature of the sample well This cone is a dummy probe 4 Place the probe assembly...

Page 265: ...witch to the 200 position 7 Turn on the GeneAmp PCR System 9600 and set up a two temperature CYCL program with the following parameters Setpoint 1 Temperature 95 C Hold Time 2 00 minutes Ramp Time 0 00 minutes Setpoint 2 Temperature 40 C Hold Time 2 00 minutes Ramp Time 0 00 minutes Cycles 99 Note Refer to Chapter 4 for detailed instructions on how to set up and run a CYCL program Artisan Technolo...

Page 266: ... read 0 30 30 seconds Record this temperature Figure 8 6 shows when to measure the temperatures Figure 8 6 Measurements in the temperature uniformity test Note You can also measure the temperature 30 seconds and one minute into Setpoints 1 and 2 if you would like to observe the dynamics of the system 95 40 Temp C Time Cycle 3 Cycle 4 Measure well A1 90 seconds into Setpoint 1 Measure well A1 90 se...

Page 267: ...over forward and turn the cover knob clockwise until the white marks are aligned 13 Repeat the measurements on wells A4 A8 A12 C1 C4 C8 C12 E1 E4 E8 and E12 H1 H4 H8 and H12 Make sure you place the measuring cone of the probe assembly into these wells and the dummy probe into adjacent wells Figure 8 7 Location of wells used in uniformity test Artisan Technology Group Quality Instrumentation Guaran...

Page 268: ...old subtract the lowest measured temperature from the highest measured temperature 2 For the 16 Setpoint 2 measurements 40 C hold subtract the lowest measured temperature from the highest measured temperature If either result is greater than 1 C your GeneAmp PCR System 9600 must be serviced by an Applied Biosystems Service Representative Artisan Technology Group Quality Instrumentation Guaranteed ...

Page 269: ...on on power requirements 1 Turn off the GeneAmp PCR System 9600 and disconnect the power cord from the instrument 2 The fuses are located next to the instrument power cord connection see Figure 8 8 Figure 8 8 Removing the fuses 3 Remove the fuse s with a screwdriver Replace the fuse s with the same type and rating of fuse 4 Replace the instrument power cord Fuse Holders Instrument Power Cord Conne...

Page 270: ...apter also explains what happens if a power failure causes the instrument to turn off while you are operating it Troubleshooting The table that begins on the following page lists instrument problems you may have the probable causes of these problems and what you can do to correct them 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 271: ...lank An internal fuse may be blown or there may be a controller problem Call an Applied Biosystems Service Engineer The displayed block temperature appears inaccurate The temperature may need to be recalibrated Perform a temperature calibration verification test using Diagnostic Test 5 and the Temperature Verification System Applied Biosystems Part No N801 0435 The heating or cooling is too slow T...

Page 272: ...eratures that are too high or too low Suspected poor cycling performance Run Diagnostic Test 4 System Performance Test then call an Applied Biosystems Service Engineer When starting a run the following display appears This is normal if you start a run just after turning the instrument on or completing a subambient hold Wait a few minutes to allow the block cover to come up to temperature If it doe...

Page 273: ...ting run time data The run time printer mode configuration parameter is not turned on Turn the run time printer mode on The printer has been in correctly set up Check the printer set up Bad Printer cable Replace the printer cable When you turn on the instrument the following display appears Possible controller failure Contact an Applied Biosystems Service Engineer Table 9 1 Troubleshooting Informa...

Page 274: ...nstrument will begin a 4 degree Hold program If you were editing a program review the History file to find out how much of your program was run before the instrument turned off see Chapter 7 If you used a printer to generate run time data time and temperature after each setpoint you can reprogram the remaining programs in the sequence required to complete the interrupted run Artisan Technology Gro...

Page 275: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 276: ...mpartment The sample compartment contains an aluminum block with 96 sample positions in an eight by twelve microplate format A heated cover over the sample vessels eliminates the need for oil Sample Tubes The sample compartment can hold 96 MicroAmp Reaction Tubes 0 2 mL 10 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 277: ...strument control panel consists of the display keypad and indicator lights Display The GeneAmp PCR System 9600 uses a 40 character blue luminescent display 20 characters x 2 lines The sample temperature is displayed in degrees Celsius to the nearest 0 1 degree C Keypad The keypad consists of nine function keys and ten numeric keys Indicator Lights There are three indicator lights Heating Cooling H...

Page 278: ...tered around the setpoint temperature two minutes after the sample temperature is within 1 degree C of setpoint Sample Block Temperature Uniformity The sample block temperature uniformity is 0 5 degrees C 30 seconds after the clock starts over the range 50 0 to 99 9 degrees C Sample Temperature Overshoot An average of 96 sample temperatures shows less than 0 5 degrees C overshoot for upramps and d...

Page 279: ...al setpoints are achieved within 5 seconds not including the first cycle Sample Heating and Cooling Rate The sample temperature ramp rate for heating and cooling is approximately one degree C per second Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 280: ...ing specifications apply Baud Rate 9600 Setup no parity 8 data bits one stop bit Temperature Calibration The GeneAmp PCR System 9600 has been calibrated to standards traceable to NIST National Institute for Standards and Technology U S Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 281: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 282: ... 5 45 displays in 5 39 5 40 5 45 last display 5 45 programming a pause in 5 43 5 44 Average block temperature calculating 8 10 8 11 B BACK key function of 5 8 moving to previous display 3 11 selecting diagnostic tests 7 36 use in directory function 7 5 use of 3 11 3 16 Base See Sample tray Beep while hold display in HOLD program 5 32 Beeper See Run time beeper 7 20 Block See Sample Block Block Cov...

Page 283: ...ndicator lights 6 16 10 2 keypad 10 2 Conventions notes and warnings S 2 P 4 used in manual S 1 P 3 Converting hold times from DNA Thermal Cycler 5 4 5 7 Cooling indicator light 6 16 Cooling samples See Sample temperature Cover knob use in sample tray installation 6 7 6 7 CREATE option on the main menu 4 4 selecting on main menu 3 8 5 10 Creating a program 5 10 Creating and editing programs 5 9 5 ...

Page 284: ...cription of 7 2 See also Diagnostic tests Diagnostic tests 7 35 7 56 Chiller Test 3 7 52 7 53 Heater Test 2 7 50 7 51 initial displays of 7 37 Review History File Test 1 7 38 7 49 selecting 7 36 7 37 by test number 7 36 using STEP and BACK keys 7 36 summary of 7 35 System Performance Test 4 7 54 7 55 test numbers of 7 35 Verify Calibration Test 5 7 56 Digital thermometer 8 4 Dimensions of instrume...

Page 285: ...Fuses changing 8 18 G GeneAmp PCR System 9600 description of software 1 5 1 6 features of 1 5 general description of 1 3 input voltages 2 4 installing 2 1 2 21 instrument specifications 10 1 10 5 Maintenance 8 1 8 18 ordering accessories and replacement parts for 2 3 parts supplied with 2 2 setting hold times 5 2 5 7 H Heated cover See Sample block cover Heater test 7 50 7 51 accessing 7 50 in ins...

Page 286: ...ht 6 16 Humidity requirements for installation 2 5 I Idle state setpoint default value 7 25 definition of 7 25 entering 7 25 If the instrument turns off 9 5 Incubation See HOLD program Hold time Indicator lights 6 16 10 2 Installation 2 1 2 21 See also Configuration parameters configuring for a printer 2 12 2 13 See also Configuration function configuring the instrument 2 14 2 16 heater and chille...

Page 287: ...mple printout 5 26 linking files in 5 18 printing 5 25 5 27 program numbers in 5 18 storing 5 21 5 22 5 24 MicroAmp reaction tubes changing the time constant 7 30 7 31 installing caps on 6 4 use in 96 position sample tray 6 2 MORE key function of 6 11 moving between two run time displays 3 26 3 26 6 18 O Offset definition of 8 11 Oil See Loading samples OPTION key changing a NO selection to YES 3 ...

Page 288: ...ter interface 10 5 Printer Kit for 115VAC printer 2 6 for 230VAC printer 2 10 Printer setup and configuration 2 6 2 13 See also Configuration function configuring for a printer 2 12 2 13 connecting printer cable 2 7 DIP switch settings and cable connections 2 9 installing 115VAC printer 2 6 Printer Kit 2 6 serial adapter card 2 6 installing 230VAC printer 2 10 connecting a plug to 230V adapter 2 1...

Page 289: ...atus records 7 39 Reviewing the history of a run 6 22 RTD probe description of 8 5 placing in sample wells A1 and A2 8 14 placing in sample wells E1 and D1 8 6 RUN key function of 6 11 RUN option description of 5 9 in System Performance test 7 55 on the main menu 4 4 use in methods 5 17 Running methods specifying a method 6 10 Running programs checking the start clock parameter 6 12 in the Tutoria...

Page 290: ...on installing 6 2 6 3 loading without samples 3 22 3 23 placing in the block 6 5 6 5 removing 6 8 Sample tray retainer installing 6 4 6 4 Sample tube reaction volume in configuration function 7 29 Sample tube time constant specifying in configuration function 7 30 7 34 Sample tube type specifying in configuration function 7 28 7 29 Sample tubes See also Loading samples MicroAmp reaction tubes in c...

Page 291: ... 3 sample compartment 10 1 sample heating and cooling rate 10 4 sample temperature accuracy 10 3 sample temperature overshoot 10 3 10 4 sample tubes 10 1 temperature calibration 10 5 Starting a run 6 11 6 16 Starting up the instrument 3 5 STAT history file display option 7 45 7 47 STAT history file print option 7 48 Status record display 7 41 in a history file 7 39 information in 7 39 messages in ...

Page 292: ...nd measurement in 8 15 Temperature uniformity 10 3 Temperature Verification System parts included 8 4 use in Verify Calibration test 7 56 Temperature requirements for installation 2 5 Test 1 See Reviewing the history file Test 2 See Heater test Test 3 See Chiller test Test 4 See System performance test Test 5 See Verify calibration test Test results of temperature calibration verification test 8 1...

Page 293: ...2 Utilities 7 1 7 61 accessing 7 2 Configuration function 7 16 7 34 Delete function 7 57 7 61 Diagnostic tests 7 35 7 56 Directory function 7 4 7 15 overview of utilities displays 7 3 selecting a utilities function 7 3 summary of functions 7 2 V Verify Calibration test 7 56 accessing 8 6 8 7 VIEW option in System performance test 7 55 Viewing a directory by program number 7 4 7 6 7 6 by program ty...

Page 294: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 295: ...nts For international office locations please call our local office or refer to our web site at www appliedbiosystems com www appliedbiosystems com 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 04 2001 Part Number 0993 8660 Rev ...

Page 296: ...l service in house repair center WE BUY USED EQUIPMENT Sell your excess underutilized and idle used equipment We also offer credit for buy backs and trade ins www artisantg com WeBuyEquipment REMOTE INSPECTION Remotely inspect equipment before purchasing with our interactive website at www instraview com LOOKING FOR MORE INFORMATION Visit us on the web at www artisantg com for more information on ...

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Applied Biosystems GeneAmp PCR System 9600, User Manual

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