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GeneAmp® PCR System 9600 - Artisan Technology Group

1. T T T T a f Epson LX 810 Printer Rear Panel 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 Figure 2 2 Side panel of the GeneAmp PCR System 9600 and rear panel of the printer showing DIP switch settings and cable connections 2 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Installing the 230 VAC Printer 2 10 The Printer Kit for the 230 VAC GeneAmp PCR System 9600 Part No N801 0314 contains a printer Part No 0942 1015 with a serial adapter card It also includes a printer cable N801 0421 and a 230 volt adapter Part No 0942 1002 To set up and install the printer proceed as follows 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 described in pages 5 38 to 5 51 of the Epson LX 810 User s Manual When using this manual pay special attention to Removing the Upper Case on page 5 38 and Installing the Board starting on page 5 44 Note the figure 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 pri
2. Loading Samples in the Tray Placing the Sample Tray in the Block Removing the Sample Tray from the Block Removing Samples from the Tray Specifying a Program 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Loading Samples The GeneAmp PCR System 9600 uses a 96 position sample tray MicroAmp Tray and retainer MicroAmp Retainer for 0 2 mL MicroAmp Reaction Tubes Using the 96 Position Sample Tray with MicroAmp Reaction Tubes To load the 96 position MicroAmp Tray follow the steps below refer to Figure 6 1 CAUTION The GeneAmp PCR System 9600 is designed for oil free operation It does not use mineral oil or glycerine in the sample block The MicroAmp Reaction Tubes fit tightly in the wells and a heated cover exerts an even pressure on all tubes No mineral oil is used on the sample surface because the heated cover eliminates condensation on the tubes 1 Place the MicroAmp Base on a flat surface such as a table Do not place the base in the sample block
3. 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 tube reaction volume start clock within parameter status message 7 39 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 40 Any one of the following messages can appear on a status record display Tube Type Xxxx Reaction Vol xxxxuL Clk starts w in x xC Start mm dd yy hh mm End mm dd yy hh mm Meth Complete Sensor Error This message shows the sample tube type and will always be the first record This message shows the reaction volume used in the run and will always be the second record This message shows the temperature at which the hold clock starts and will always be the third record This message shows the date and time the run began and will always be the fourth record This message shows the date and time the run ended This message will always appear at the end of a successful method run This message will appear if the sample block temperature was read incorrectly ten times in a row This is a fatal error message Artisan Technology
4. 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 223055 i0tsoencsevtvisebedewd 3 20 Starting a Trial RUN coe edsees ie itiietisestiaus 3 22 Loading a Tray without samples 3 22 Running the Program 3 24 The Next Step abide sidi distillerie thidesetara ce 3 27 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 4 Software Basics 4 1 INMTOULICUION 223403 ia ssmee bees sseeus Reeder baees 4 1 Reviewing Keypad Basics 4 2 Use of the KeyS 2iic05 seek ee award das de dima wae eee 4 3 A Close Look at the Main Menu 4 4 Selecting a Function 4 tee eeeies eda eGaees wd oes 4 5 An Overview of PCR Programs and Methods 4 6 Linking Programs ina PCR Method 4 6 Storing Programs and Methods 4 7 The HOLD Program 2 42 4442265 1356454664550 dha005846 piia 4 8 CYCL The Cycle Program 4 10 The AUTO Program 22 2 22488 senor needa uanes dada 4 12 PCR Methods 562 4icdst2es dtd ous degeadeihisscavarne de 4 14 Chapter 5 Setting Up PCR Programs and Methods
5. 5 1 101068 VTC 1 siecia oei sah aseeead amp ae acess esa ao ee E 5 1 Setting Hold Times on the GeneAmp PCR System 9600 5 2 Editing KEYS ass eea crain aada ana aia Wiebe ra Rees 5 8 Creating and Editing Programs 5 9 Creating a Program 5 10 Storing the Program 5 11 Editing a PrOgFAM 25 25 beetetdsses be beneereee bese 5 13 Printing a PIOOrais2 53 4224 see IR eG 244458358040 eR bees 5 16 Creating and Editing Methods 5 17 Creating a Method 5 18 Storing the MeINOd isu34 0554atseshienrevisabavesebed 5 21 Editing a Method 2 5 lt c1 2syeen see etbine miatt adan ja 5 23 Printing a Method 5 25 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 6 Software Shortcuts 5 28 Using the STOP Key 5 28 Recalling Programs A Shortcut 5 30 The HOLD Program i0c4sesues pean seat eee tases aba was 5 31 The Displays ina HOLD Program 5 31 Description of HOLD Program Displays 5 32 CYCL The Cycle Program 5 33 The Displays ina CYCL Program 5 33 Description of CYCL Program Displays 5 34 The AU
6. CAUTION Do not place the MicroAmp Base in the sample block Figure 6 3 Placing the sample tray in the block 6 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com which fully raises the platen before you attempt to slide the 2 Make certain that the cover knob is completely counterclockwise heated cover forward Then slide the cover forward Top View Side View Cover Knob Heated Platen Full counterclockwise position Figure 6 4 Sliding the heated cover forward Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com lines up with the white mark on the cover indicating the full E Turn the cover knob clockwise until the white mark on the knob clockwise position This lowers the platen onto the tray Top View Side View Cover Knob Full clockwise position Figure 6 5 Turning the cover knob Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 6 7 Using the Cap Installing Tool Use the MicroAmp Cap Installing Tool supplied with your instrument to cap a single sample tube or a row of sample tubes as described in the following procedure 1 Place individual sample tubes or a row of tubes in the sample tray you don t have to use a retainer 2 Manually press the cap s onto the tube s so that the caps are not sitting loosely on the tu
7. Chiller Test Passed 3 Press STOP to exit the test The next test Test 4 will appear on the display Press STOP again to return to the Utilities menu 2 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Tutorial Customizing a PCR CYCL Program Introduction This tutorial explains how to set up a time and temperature profile for PCR To do this you will customize the CYCL Cycle program stored in instrument memory Follow the instructions in this tutorial step by step and you will learn how to start the instrument 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 fora PCR profile and start a run Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 2 Before You Start Before you start this tutorial 1 The system should be properly installed either by an Applied Biosystems service representative or according to the supplied instructions in Chapter 2 Installati
8. 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 through H from back to front Note The above procedure is most useful if you are loading a dozen or more samples If you are only loading a few samples use the sample tray base as a working tray in which to load your sample tubes then transfer your tubes to a sample tray already loaded in the instrument Do not use the MicroAmp Retainer if you want to remove a single tube without removing the caps from all the tubes The caps will not fit through the retainer 6 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com MicroAmp Retainer Sirip of 12 caps Tab MicroAmp MicroAmp Reaction Tubes one row shown Sample Tray Cutout always to left Table or Other Flat Surface necessary to support base Setting up the 96 position sample tray Figure 6 1 6 3 Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Instrumentation Note When using MicroAmp Reaction Tubes with Caps place the required number of tubes into
9. DEFAULTS will change to MODIFY Pressing the OPTION key again will change MODIFY back to NO Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 Press ENTER The following display appears Rxn vol 100uL T 9 5 Rxn vol 50uL T 7 0 This display lets you change the sample tube time constant There are two default values for sample tube time constants on this display one for sample tubes with a reaction volume of 100 UL and one for sample tubes with a reaction volume of 50 uL There is a time constant default value for sample tubes with a reaction volume of 20 uL that appears on a separate display Press STEP to view this display Rxn vol 20uL T 5 0 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 the first Configuration display 7 31 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com THIN Time Constant This parameter works the same way as the MICRO time constant except that the default time constant values are different Change the sample tube time constant value for Thin Walled GeneAmp Reaction Tubes as fol
10. Guaranteed 888 88 SOURCE www artisantg com Item Part No Quantity 230 220V Conversion Kit N801 0110 1 shipped with 230V unit 100V 50Hz to 60Hz Conversion N801 0111 1 Kit shipped with 100V unit PCR System 9600 Video N801 0661 1 Domestic and Japan PCR System 9600 Video N801 0660 1 Europe Users Manual 0993 8660 1 Quick Reference Guide 0993 8690 1 Brochures 0993 8813 1 Supplies Accessories and Replacement Parts For Sales Assistance and Information 1 800 345 5224 For Technical Assistance 1 800 762 4001 Supplies accessories and replacement parts can be ordered directly from Applied Biosystems using the eight digit part numbers provided in this manual Applied Biosystems catalog service offers a full selection of high quality instrumentation reagents and consumables through the Biotechnology Catalog To place an order 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 2 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Power Requirements CAUTION Before the power is turned on for the first time at installation be sure that the unit has been upright for at least four hours at normal indoor temperatures 15 degrees C to 30 degrees C Th
11. lectriques d brancher le cordon d alimentation avant le d pannage CAUTIONThis unit contains protective circuitry Contact Applied Biosystems Service before performing any AC line tests AVERTISSEMENT Cet appareil contient des circuits de protection V rifier aupr s de Applied Biosystems avant d effectuer des essais de secteur S 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com S 6 WARNING Hot Surface Use care when working around this area to avoid being burned by hot components AVERTISSEMENT Surface chaude WARNING To reduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour r duire le risque de chocs lectriques ne pas ouvrir les couvercies si un outil est n cessaire Ne contient aucune pi ce pouvant tre r par e par l utilisateur Confier le d pannage au personnel qualifi de Applied Biosystems Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com WARNING For protection against fire hazard replace only with same type and rating of fuse AVERTISSEMENT Afin d assurer la protection contre les risques d incendie remplacer uniquement par un fusible de m me type et de m me courant nominal LEFT S
12. tropix appliedbiosystems com In the United States and Canada technical support is available at the Telephone following times Technical Support S 14 Artisan Technology Group Quality Instrumentation Product Hours Chemiluminescence 8 30 a m to 5 30 p m Eastern Time Framingham support 8 00 a m to 6 00 p m Eastern Time All Other Products 5 30 a m to 5 00 p m Pacific Time Guaranteed 888 88 SOURCE www artisantg com To Contact Technical Support by Telephone or Fax Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com In North America To contact Applied Biosystems Technical Support use the telephone or fax numbers given below To open a service call for other support needs or in case of an emergency dial 1 800 831 6844 and press 1 Product or Product Area Telephone Dial Fax Dial ABI PRISM 3700 DNA Analyzer 1 800 831 6844 then press 8 1 650 638 5981 DNA Synthesis 1 800 831 6844 then press 21 1 650 638 5981 Fluorescent DNA Sequencing 1 800 831 6844 then press 22 1 650 638 5981 Fluorescent Fragment Analysis includes GeneScan applications 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
13. 3 Press the OPTION key three times to move the cursor to PRINT then press ENTER The following display appears PRINT HISTORY ALL STAT ERRORS 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Press OPTION to move the cursor to your desired selection then press ENTER The following display appears History Print printing Figure 7 13 shows a History file printout of all status and data records ALL for a CYCL program AB GeneAmp PCR System 9600 Ver 2 June 1 1992 12 00 pm History File Rec Program CYCL CYCL CYCL CYCL CYCL CYCL CYCL CYCL CYCL CYCL CYCL OMAN DOP WN 4 H pa e o 3 3 3 3 3 3 3 3 3 3 3 Status Temp Time Cyc Setpt Tube type is MICRO Reaction volume is 100uL Start clock within 1 0C of setpoint Run Start June 1 1992 11 24 am 94 1C 1 54 1 1 67 9C 0 52 1 2 94 1C 1 11 2 1 67 9C 0 52 2 2 94 1C 1 11 3 1 67 9C 0 52 3 2 Run Complete June 1 1992 11 31 am Figure 7 13 Printout of all status and data records ALL of a typical History 7 49 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Runni
14. 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 Biolnformatics includes BioLIMS BioMerge and SQL GT applications 1 800 831 6844 then press 25 1 505 982 7690 Peptide Synthesis 433 and 43X Systems 1 800 831 6844 then press 31 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 then press 32 1 650 638 5981 PCR and Sequence Detection 1 800 762 4001 then press 1 for PCR 2 for the 7700 or 5700 6 for the 6700 or dial 1 800 831 6844 then press 5 1 240 453 4613 S 15 S 16 Product or Product Area Telephone Dial Fax Dial Voyager MALDI TOF Biospectrometry and Mariner ESI TOF Mass Spectrometry Workstations 1 800 899 5858 then press 13 1 508 383 7855 Biochromatography BioCAD Workstations and Poros Perfusion Chromatography Products 1 800 899 5858 then press 14 1 508 383 7855 Expedite Nucleic acid Synthesis Systems 1 800 899 5858 then press 15 1 508 383 7855 Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5858 then press 15 1 508 383 7855 PNA Custom and Synthesis 1 800 899 5858 then press 15 1 508 383 7855 FMAT 8100 HTS System and Cytofluor 4000 Fluorescence Plate Reader 1 800 899 5858 then press 16 1 508 383 7855 Chemiluminescence Tropix 1 8
15. 8 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Cleaning the Heated Cover The heated cover should be cleaned once a month or as needed WARNING During instrument operation the heated cover can be heated as high as 107 degrees C Before performing the following procedure be sure to wait until the sample block reaches room temperature To clean the heated cover proceed as follows 1 Run a 25 degree HOLD program to bring the sample block to room temperature then turn off the instrument for 15 minutes Rotate the heated cover handle counterclockwise and slide the cover about 1 3 of the way towards the back of its range 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 Soak a clean cloth with isopropanol and gently wipe the bottom of the cover Remove any remaining isopropanol from the cover and replace the cover in its rail Remember the rail is notched about 1 3 of the way towards the back of its run If the heated cover becomes contaminated remove the cover as described above and wipe the bottom of the cover with a cloth soaked in Chlorox 8 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Temperature Calibration Verifica
16. A rtisan Artisan Technology Group is your source for quality TecmoogyGroup new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Experienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment 7 EQUIPMENT DEMOS HUNDREDS OF InstraV ea REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com information on price quotations drivers technical LEASING MONTHLY specifications manuals and documentation RENTALS ITAR CERTIFIED DL A UT DU Contact us 888 88 SOURCE sales artisantg com www artisantg com GeneAmp PCR System 9600 User s Manual Applied KS Biosystems Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Copyright 2001 Applied Biosystems All rights reserved For Research Use Only Not for use in diagnostic procedures Notice AUTHORIZED THERMAL CYCLER NOTICE This GeneAmp PCR System 9600 is an Authorized Thermal Cycler Its purchase price includes the up front fee component of a license under the patents of the Polymerase
17. Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 58 The following display appears Delete Enter program xxx xxx on the display pictured above represents the program number of the program you want to delete 3 Press the numeric keys that correspond to the number of the program 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Deleting Programs by User Number To delete all of the programs stored under a specified user number 1 Select DEL on the Utilities menu as described on page 7 3 The following display appears Delete PROGRAM USER ALL Press the OPTION key to move the cursor to USER then press ENTER The following display appears Delete Enter user xxxx 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 Progs linked in meth STEP to list progs 4 Press the STEP key to scroll through the list of linked programs 7 59 Artisan T
18. The Displays in a CYCL Program Figure 5 9 shows the main displays that make up a CYCL program 3 Temperature PCR Setpt 1 Ramp 0 00 94 0C Hold 0 30 moves you Setpt 2 Ramp 0 00 forward to the 55 0C Hold 0 30 next display k Back Setpt 3 Ramp 0 00 Back 72 0C Hold 0 30 moves you to the previous display or Total cycles 25 parameter Pause during run NO CYCL 20 xx xC Press fo return fo the RUN STORE PRINT HOME Step fist display Figure 5 9 The main displays in a three temperature CYCL program 5 33 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 Temperature PCR Setpt 1 Ramp 0 00 94 0C 5 34 Hold 0 30 Description of CYCL Program Displays Defines the number of incubation temperatures or setpoints used in the PCR cycle A typical PCR cycle consists of three 3 setpoints therefore 3 is the default value Press ENTER to accept the default or type a different number 1 9 then press ENTER Setpoint 1 in a typical cycle program is used for DNA denaturation or melting This display sets the following values for the first setpoint Setpt 1 Setpoint temperature 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 sampl
19. This display lets you change the sample tube time constant There are two default values for sample tube time constants on this display one for sample tubes with a reaction volume of 100 uL and one for sample tubes with a reaction volume of 50 uL There is a time constant default value for sample tubes with a reaction volume of 20 uL that appears on a separate display Press STEP to view this display Rxn vol 20uL T 5 0 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 the previous display Or press STOP to return to the first configuration display From here you can return to the main menu by pressing STOP twice 2 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 18 There are two additional configurable parameters that let you change the time constants for 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 Heater and Chiller Tests Heater Test After you have configured the GeneAmp PCR System 9600 perform the heate
20. www artisantg com Users Manual Summary If You Have Used the Applied Biosystems DNA Thermal Cycler or DNA Thermal Cycler 480 Describes the differences between the GeneAmp PCR System 9600 and the DNA Thermal Cycler DNA Thermal Cycler 480 Preface Describes how to use this manual Chapter 1 Introducing the GeneAmp PCR System 9600 Describes instrument operation the hardware and the software Chapter 2 Installation Describes how to install the instrument 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 how to create PCR methods Chapter 6 Running PCR Samples Describes how to load samples and start a run Describes the run time keys and displays Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 7 Utilities Describes how to obtain a history of the run configure the instrument run diagnostics and update the file directory Chapter 8 Maintenance Describes periodic maintenance procedures Chapter 9 Troubleshooting Describes how to solve common problems and what to do in case of
21. 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 configuration function 7 28 installing caps on 6 4 removing from sample tray 6 9 6 9 selecting type before a run 6 12 6 13 Sample wells used in temperature calibration verification test 8 5 8 6 used in temperature uniformity test 8 14 8 16 8 16 8 16 Samples heating and cooling rate of 10 4 loading 6 2 6 4 removing 6 9 Selecting a print mode 6 14 available print options 6 14 Selecting a utilities function 7 3 Serial adapter card in printer installation 2 6 2 7 setting DIP switches on 2 6 2 8 Setpoint clock 7 26 changing the temperature interval 7 26 temperature interval Index 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com default value 7 26 temperature interval 7 26 7 26 SETPOINT print option example printout 6 15 SETPOINT print option 6 14 Setpoint time See Hold time Ramp time Setpoints defining number in AUTO program 5 40 defining number in CYCL program 5 34 in AUTO program automatic incrementing and decrementing of 5 41 specifying a pause after 5 44 in CYCL program specifying a pause after 5 37 in CYCL programs 3 3 Setti
22. 88 SOURCE www artisantg com Getting to the CYCL Program 1 After you start the instrument the main menu shown below appears on the screen Select Option 9600 RUN CREATE EDIT UTIL Think of the main menu as your home base It gives you access to the major functions of the instrument You can easily get to the main menu from any of the other displays by pressing 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 Select Option 9600 RUN CREATE EDIT UTIL Cursor The cursor marks the current selection on the display 3 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 To select an option on the main menu you use the OPTION key To learn how the OPTION key works follow these steps a Press the OPTION key to move the cursor from one selection to the next Select Option 9600 RUN CREATE EDIT UTIL to move Option the cursor to the next selection b When the cursor reaches the last selection UTIL press OPTION to move the cursor to the first selection again Select Option 9600 RUN CREATE EDIT UTIL Press To move the cursor to here The OPTION key is used the same way on many different displays 3
23. 88 SOURCE www artisantg com In the example below the temperature was decreased by 22 degrees C This value was rounded to 20 degrees C According to Table 5 2 with a starting temperature of 94 degrees C we should subtract 53 seconds from the hold time on the DNA Thermal Cycler giving us a new hold time of 27 seconds DNA Thermal Cycler gt GeneAmp PCR System 9600 Temp ers Temp 670 C Starting Temp 94 C Starting Temp 94 94 94 A femp 22 round 72 72 Hold to 20 80 sec 27 sec Time Time 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 5 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Editing Keys 5 8 To create view or edit programs and methods you will use the following keys Back Enter OOL M JUUL Er JUL Stop Figure 5 4 Editing Keys The function of each key is described below BACK Moves the cursor to the previous parameter or display STEP Moves the cursor 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 pr
24. A shortcut to the above procedure is 1 With any of the program displays shown press STOP The following display appears CYCL xx xC RUN STORE PRINT HOME 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 29 Recalling Programs A Shortcut 5 30 Once you have finished editing or running a program you can quickly recall another program without needing to return to the main menu 1 Once you have stored a program your display will look like this CYCL program shown Program oo Number 26 CYCL 26 xx xC RUN STORE PRINT HOME 2 Although the cursor appears under RUN at this point you can enter any program number The program number you enter will appear on the top line Then press ENTER Note Ifthe 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 beginning of the program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE
25. Back Pause Stop There are two types of keys run time keys and editing keys Run time keys are used while running samples for example to start 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 Run time key Starts or restarts a sample run Editing key Moves the cursor to the pre vious parameter or display Run time key Interrupts a run Run time and Editing key Run time Aborts a run Editing Returns you to the last display in a program or fo the main menu Enter More Step Option CE Run time key Displays more information about run time parameters Editing key Moves the cursor to the next parameter or display Editing key Moves the cursor to your se lection Changes a YES response to a NO and vice versa Editing key Clears the current numeric entry Editing key Accepts the selection marked by the cursor 4 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com A Close Look at the Main Menu Select Option 9600 RUN CREATE EDIT UTIL The main menu shown above appears a few seconds after the instrument is first turned on If the instrument is already on and the main menu is not shown you can always access the main
26. This display shows the main menu Select Option 9600 RUN CREATE EDIT UTIL In displays where the current temperature of the samples is indicated the temperature is shown in the manual as xx xC as in the display below CYCL 26 xx xC PAUSE 10 00 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 P 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Notes and Warnings P 4 The following conventions are used in this manual WARNING A warning indicates an operation that could cause 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 Introducing the GeneAmp PCR System 9600 Introduction This chapter describes the principles of instrument operation the hardware and the software Figure 1 1 The GeneAmp PCR System 9600 Artisan Technology Group Qual
27. all your HOLD programs will be printed Directory Print Enter User 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 As your directory is printed the following display appears Directory Print printing When printing is complete the first Print display appears Press STOP to the return to the Directory display Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Figure 7 5 shows all the displays in the PRINT selection of the Directory function Directory Print PROG TYPE USER Press Directory Print Enter program Directory Print printing Directory Print HOLD CYCL AUTO METH Press to return to the Directory display Press to return to the Directory display Directory Print printing to retum fo the Directory display Directory PROG TYPE USER PRINT Figure 7 5 The PRINT selection of the Directory function 7 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Configuration Function CONFIG The Configuration function lets you customize the instrument by editing the configuration parameters These parameters include time and date run time printer mode on or off run time beeper
28. scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 04 2001 Part Number 0993 8660 Rev E an Applera business Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com A rtisan Artisan Technology Group is your source for quality TecmoogyGroup new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Experienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment 7 EQUIPMENT DEMOS HUNDREDS OF InstraV ea REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com information on price quotations drivers technical LEASING MONTHLY specifications manuals and documentation RENTALS ITAR CERTIFIED DL A UT DU Contact us 888 88 SOURCE sales artisantg com www artisantg com
29. 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 6 16 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Run Time Displays During a run you will see a run time display that is continuously updated for the program being run CYCL and AUTO Program Run Time Displays The run time displays for a CYCL program and an AUTO program are the same If you are in a ramp segment the display will show Ramp to If you are in a hold segment the display will show Hold at These displays are shown in Figure 6 9 Setpoint temperature Current sample temperature Ramp to 94 0C xx xC 0 00 Cycle 1 Current cycle counts up cycles during a run Time remaining Setpoint temperature Current sample temperature Hold at 94 0C xx xC 0 12 Cycle 1 Current cycle counts up cycles during a run Time remaining 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 6 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Ramp to 94 0C xx xC 0 30 Cycle 1 To move between the two run time displays
30. 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The cursor moves to the hold time Setpt 1 Ramp 0 00 96 0C Hold 0 30 4 Sometimes you may want to change an entry after you have pressed ENTER To move back to the previous entry you press the BACK key The cursor is now at the hold time Press BACK to move the cursor back to the temperature Setpt 1 Ramp 0 00 94 0C Hold 0 30 To move the cursor back to the previous parameter 5 Now 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 2 Ramp 0 00 55 0C Hold 0 30 3 16 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Defining Values for Setpoint 2 Setpt 2 Ramp 0 00 55 0C Hold 0 30 1 Use the default ramp time by pressing ENTER 2 Enter 52 5 degrees C for the temperature by pressing 5 then 2 then 5 Then press ENTER 3 We will not change the hold time Press STEP to skip over this entry The display for Setpoint 3 appears Defining Values for Setpoint 3 Setpt 3 Ramp 0 00 72 0C Hold 0 30 1 Use the default ramp time by pressing ENTER Enter 74 5 degrees C for the temperature Press ENTER We will not change the hold time Press STEP to skip over this entry and m
31. 2 Problem The power switch is on but there is no response There is no display on the screen and no noise from the motor or fan Power is on but the screen is blank and the motor is running Or when you press a key the display does not show the appropriate response or the screen is blank The displayed block temperature appears inaccurate The heating or cooling is too slow Possible Cause The power cable is loose or not plugged in Fuse is blown An internal fuse may be blown or there may be a controller problem The temperature may need to be recalibrated There is a possible controller or mechanical malfunction Check and or Remedy Plug the power cable in properly Replace the fuse Call an Applied Biosystems Service Engineer Perform a temperature calibration verification test using Diagnostic Test 5 and the Temperature Verification System Applied Biosystems Part No N801 0435 Run Diagnostic Test 2 Heater Test and 3 Chiller Test Call an Applied Biosystems Service Engineer if either test fails Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Table 9 1 Problem The system will not cool down to subambient temperatures An error message is displayed when you turn on the instrument You are getting unexpected or unrepeatable cycle times or temperatures that are too high or too low When s
32. 2 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 has software version 1 05 or higher press STOP to return to the first Configuration display 7 33 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com CAUTION If your instrument has software version 1 04 or lower configure the THIN tube time constant for a default response time of 12 0 seconds for 20 uL reaction volume When initiating a PCR program specify a reaction volume of 20 uL for all experiments using Thin Walled GeneAmp Reaction Tubes If your instrument has software version 1 05 or higher the response time of 12 0 seconds for all three reaction volumes is correct for the Thin Walled GeneAmp Reaction Tubes Printing the Configuration Parameters 7 34 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 Configuration EDIT PRINT 2 Press OPTION to move the cursor to PRINT then press ENTER As the configuration parameters are printed the following display appears Configuration printing 3 When printing has been completed the first Conf
33. 7 55 test numbers of 7 35 Verify Calibration Test 5 7 56 Digital thermometer 8 4 Dimensions of instrument 10 1 DIP switches on printer 2 6 2 9 on serial adapter card 2 6 Directory function 7 4 7 15 description of 7 2 directory display 7 4 selecting the PROG option 7 4 selecting the TYPE option 7 7 selecting the USER option 7 10 example directory listed by program number 7 6 example directory listed by program type 7 9 example directory listed by user number 7 12 listing programs by program number 7 4 7 6 listing programs by program type 7 7 7 9 listing programs by user number 7 10 7 12 PRINT selection displays 7 15 Printing a directory 7 13 7 15 returning to main menu from 7 4 types of directories 7 4 Index 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Displayed sample temperature 10 3 Documents on Demand S 19 Dot matrix printer See Printer setup and configuration E Edit function 5 13 EDIT option See also Editing programs See also Editing programs on the main menu 5 13 Editing configuration parameters 7 16 7 17 Editing keys 4 3 4 3 5 8 description of 5 8 5 8 Editing methods 5 23 5 25 Editing programs 5 13 5 15 EDIT option on the main menu 4 4 overwriting 5 15 storing 5 14 Electrical power See Power requirements E mail address for technical support S 14 ENTER key
34. 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 Enter Diag Test 1 REVIEW HISTORY FILE 2 Select Diagnostic Test 4 by pressing 4 then pressing ENTER or by pressing the STEP key three times The following display appears Enter Diag Test 4 SYSTEM PERFORMANCE Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 Press ENTER The following display appears System Performance VIEW RUN PRINT This display lets you choose one of the following options VIEW Select this option to view the last test results on a series of displays Use the STEP key to move forward through the displays use the BACK key to move backward through the displays RUN Select this option to run the test PRINT Select this option to print a list of the test results 4 Press the OPTION key once to move the cursor to RUN on the display then press ENTER The test will begin and will take about a half hour to complete 5 After the System Performance Test has been completed press ENTER with the cursor under the VIEW selection to view the test results OR Press the OPTION key twice to move the cursor to the PRINT selection then press ENTER A list of the test results will be printed 6 Review the test results with an Applied Biosystems Service Engineer The Service Eng
35. Blk xx x going to 50C The value xx x on the screen pictured above represents the current temperature in degrees C of the sample block When the temperature stabilizes the system 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 Chiller Test Passed 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 7 53 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Running the System Performance Test 7 54 Diagnostic Test 4 is the System Performance Test The System Performance Test is a series of comprehensive tests of the instrument s heating and cooling systems and is used to help an Applied Biosystems Service Engineer diagnose any special problem you may be having with your GeneAmp PCR System 9600 Run this test when you suspect problems with the instrument and the Heater Test and Chiller Test both pass The System Performance takes about 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
36. Chain Reaction PCR process which are owned by Roche Molecular Systems Inc and F Hoffmann La Roche Ltd to practice the PCR process for internal research and development using this instrument The running royalty component of that license may be purchased from Applied Biosystems or obtained by purchasing Authorized Reagents This instrument is also an Authorized Thermal Cycler for use with applications licenses available from Applied Biosystems Its use with Authorized Reagents also provides a limited PCR license in accordance with the label rights accompanying such reagents Purchase of this product does not itself convey to the purchaser a complete license or right to perform the PCR process Further information on purchasing licenses to practice 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 PARTICULAR PURPOSE APPLIED BIOSYSTEMS SHALL NOT BE LIABLE FOR ERRORS CONTAINED HEREIN OR FOR INCIDENTAL CONSEQUENTIAL DAMAGES IN CONNECTION WITH THE FURNISHING PERFORMANCE OR USE OF THIS MATERIAL Release Information Manual Manual Part No Version 0993 8660 04 2001 Trademarks Applied Biosyst
37. External Fuses There are two slow blow fuses accessible from the left side of the instrument Use the following procedure to change these fuses Use 15 Amp slow blow fuses for the 100 and 120 VAC instruments Use 8 Amp slow blow fuses for the 220 240 VAC instruments See Chapter 10 for information 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 Fuse Holders Instrument Power Cord Connection F1 F2 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Troubleshooting Introduction This chapter contains troubleshooting information to help you correct any problems you experience in operating the GeneAmp PCR System 9600 This chapter 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Table 9 1 Troubleshooting Information 9
38. Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Starting the Run Run Keys The following keys are used to start a run or are used during the run Run More Pause line Stop OWL ER JUUL Figure 6 7 Run Time Keys The 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 6 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Running a Stored Program 6 12 To run a program that you have previously stored 1 Access the main menu Select Option 9600 RUN CREATE EDIT UTIL CAUTION Before you start a run make sure the Start clock within x xC of setpoint parameter in the Configuration function is set correctly To do this select UTIL on the main menu then select CONFIG on the Utilities menu Press ENTER then press the STEP key five times to view the Start clock parameter See Chapter 7 for complete instructions 2 With the cursor positioned under RUN press ENTER The following display appears Run Enter program 3 Select the desired program by pressing the appropriate numeric keys then ENTER The following display appears Select tube MICRO Reaction vol 100uL This display lets yo
39. Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setting Hold Times on the GeneAmp PCR System 9600 These general guidelines are based upon differences in how the instruments operate to heat and cool samples The hold times that you specify in your PCR CYCL and AUTO programs for the GeneAmp PCR System 9600 will be shorter than those you used for your Step Cycle or Thermo Cycle files on the DNA Thermal Cycler This is because the Thermal Cycler starts counting the hold 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 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 minute or greater is required on the DNA Thermal Cycler for the samples to reach the target temperature On the GeneAmp PCR System 9600 hold times of less than one minute are often used Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com DNA Thermal Cycler 480 Hold Time 94 93 Temp C Time Clock starts 1 minute when block reaches target temperature GeneAmp PCR System 9600 Hold Time 94 93 Temp 9C Time Clock starts when
40. OPTION key changing a NO selection to YES 3 18 3 18 function of 5 8 selecting options on main menu 3 7 3 7 selecting utilities functions 7 3 Ordering replacement parts 2 3 Overshoot 10 3 10 4 Overwriting programs 5 15 Overwriting protected programs 5 15 P Pause during run in AUTO program 5 43 in CYCL program 5 36 PAUSE key function of 6 11 Pause time out limit acceptable range 7 22 changing 7 22 default value 7 22 definition of 7 22 Pausing a run 6 20 PCR method definition 4 6 description of 4 14 example of 4 14 Index 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com PCR programs and methods overview of 4 6 4 7 setting up 5 1 5 45 PCR technique annealing step 1 2 Denaturing step 1 2 description of 1 2 Extending step 1 2 in AUTO program 4 12 in CYCL program 4 10 in HOLD program 4 8 in methods 4 14 Polymerase chain reaction definition of 1 2 Power interruption 9 5 Power requirements 2 4 2 5 10 2 input voltages 2 4 Power switch location of 3 5 Precautions 2 5 Primer annealing See PCR technique Primer extending See PCR technique PRINT on directory display 7 15 on the directory display 7 13 7 15 PRINT HISTORY display 7 47 PRINT history file option 7 45 Print mode available options 6 14 CYCLE option 6 14 OFF option 6 14 SETPOINT option 6 14 PRINT option See also Printing program
41. Parts Supplied Power Requirements Proper Location Operating Precautions Printer Setup and Configuration optional Heater and Chiller Tests Configuring the System Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Unpacking Parts Supplied 2 2 Inspect the GeneAmp PCR System 9600 and all other parts supplied for any damage that may have occurred during shipment If there has been any damage during transit notify the carrier and Applied Biosystems immediately Save the shipping container and all packing materials in case it becomes necessary to reship the instrument Do not attempt to lift or move the instrument without the assistance of others Safety training for proper lifting techniques is recommended WARNING Improper lifting can cause painful and sometimes permanent back injury Use proper lifting techniques when lifting or moving the instrument The following parts are supplied with the GeneAmp PCR System 9600 Item Part No Quantity PCR System Starter Kit N801 0538 1 Consumable items for instrument operations Line Cord Domestic 120V N801 6033 1 Line Cord Continental Europe 0999 1401 1 220V 230V Line Cord Japan 100V 0999 1420 1 15 Amp slow blow Fuse 0998 1756 2 system fuse for 100 120V units 8 Amp slow blow Fuse system 0998 1643 2 fuse for 220 230V units Artisan Technology Group Quality Instrumentation
42. 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 FILE 7 36 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 Press STEP to scroll forward through the remaining four Diagnostic test displays press BACK to scroll backward through all four of the test displays Press STOP at any time to return to the Utilities menu Figure 7 8 shows the initial displays for the diagnostic tests Press Enter Diag Test 1 Step REVIEW HISTORY FILE to move to the next display Enter Diag Test 2 HEATER TEST Press Enter Diag Test 3 ac CHILLER TEST to move to the previous display ERASERS Enter Diag Test 4 Press SYSTEM PERFORMANCE Enter Diag Test 5 anytime to return to YERIFY CALIBRATION the Utilities menu Figure 7 8 Initial displays for the five diagnostic tests The following sections describe each diagnostic test in detail Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Reviewing the History file Diagnostic Test 1 lets you review the History file for the most recent run About The History File The History file records
43. Then refer to Getting to the CYCL Program on page 3 6 3 Temperature PCR 2 inthis 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 of 3 The display for Setpoint 1 appears Setpt 1 Ramp 0 00 94 0C Hold 0 30 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Defining Values for Setpoint 1 Setpt 1 Ramp 0 00 94 0C Hold 0 30 In the following steps you will change some of the default values for Setpoint 1 1 Look for the cursor on the display It appears under the ramp time The default time of 0 00 is most commonly used This causes the sample to be heated or cooled to the target temperature as fast as possible For this example we will not change the default ramp time Press ENTER to accept 0 00 minutes The cursor moves to the temperature entry Setpt 1 Ramp 0 00 94 0C Hold 0 30 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 press 9 then 4 then 0 3
44. When the desired response is displayed press ENTER Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Pause after setpt 1 Beep while pause YES lst pause at cyc 1 Pause every 25 cyc s Pause time 10 00 The display appears only if you specified a pause in the previous display In this display you define the setpoint after which you want to pause the run Type the number of the desired setpoint then press ENTER During the pause you specify whether or not you want a beeper to sound Press the OPTION key to change the YES default to a NO and vice versa When the desired response is displayed press ENTER This display only appears if you specified a pause during the run In this display you specify the number of the cycle in which you want the run to pause The default value 1 indicates that the instrument will pause during the first cycle 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 other cycle press 2 After you specify the number press ENTER This display only appears if you specified a pause during the ru
45. a MicroAmp Base then fill each tube with PCR reagents and close the caps firmly Position an empty MicroAmp Tray in the sample block then place the MicroAmp Reaction Tubes with Caps into the MicroAmp Tray sitting in the sample block 4 Place the MicroAmp Retainer over the sample tray and tubes see Figure 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 Pipette the PCR reaction mixture into the sample tubes 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 8 for additional instructions on how to cap your sample tubes L LE Retainer Tray gt Base Figure 6 2 Securing the retainer on the tray 6 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing the Sample Tray in the Block Lift the sample tray and retainer assembly from the sample tray base and place it in the sample block Make certain that the notch in the sample tray is at the left of the 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 A Notch is on left side not shown
46. and one for sample tubes with a reaction volume of 50 uL There is a time constant default value for sample tubes with a reaction volume of 20 uL that appears on a separate display Press STEP to view this display Rxn vol 20uL T 5 0 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 7 Press STOP to return to the first Configuration display 7 29 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setting Sample Tube Time Constants 7 30 There are two additional parameters in the Configuration function that let you change the time constants for MicroAmp Reaction Tubes and Thin Walled GeneAmp Reaction Tubes We recommend that you do not change the time constant values unless instructed to do so by future documentation MICRO Time Constant To change the sample tube time constant value for MicroAmp Reaction Tubes 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER then press STEP until the following display appears Set MICRO tube time constants NO 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
47. artisantg com Sample Temperature Range The temperature range of the sample block is 4 0 degrees to 99 9 degrees C Sample Temperature Accuracy The displayed sample temperature matches the average true sample temperature within 0 75 degrees C Displayed Sample Temperature The displayed sample temperature will match the specified setpoint temperature to within 0 2 degrees C centered 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 downramps Figure 10 1 illustrates block temperature overshoot after ramping up 10 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Target Temperature Sample Temperature Time Figure 10 1 Sample temperature overshoot after ramping up Ramp Time Repeatability Thermal 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 10 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www a
48. asked questions and for more information about our Through the Products You can also order technical documents or an index of Internet 2Vailable documents and have them faxed or e mailed to you through our site The Applied Biosystems Web site address is http www appliedbiosystems com techsupp To submit technical questions from North America or Europe Step Action 1 Access the Applied Biosystems Technical Support Web site 2 Under the Troubleshooting heading click Support Request Forms then select the relevant support region for the product area of interest 3 Enter the requested information and your question in the displayed form then click Ask Us RIGHT NOW blue button with yellow text 4 Enter the required information in the next form if you have not already done so then click Ask Us RIGHT NOW You will receive an e mail reply to your question from one of our technical experts within 24 to 48 hours S 18 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com To Obtain Free 24 hour access to Applied Biosystems technical documents Documents on including MSDSs is available by fax or e mail or by download from our Demand Web site To order documents Then by index a Access the Applied Biosystems Technical Support number Web site at http www appliedbiosystems com techsupp Click the Index link for the document type
49. begins Enter Diag test 2 HEATER TEST If Heater Test Passed appears 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 Heater Test Passed 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chiller Test The chiller test verifies that the refrigeration system is operating correctly CAUTION Before you begin this test make sure you place 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 The following display should appear If not follow Steps 1 through 3 in the heater test procedure on page 2 19 Enter Diag test 1 REVIEW HISTORY FILE 2 To access the chiller test press 3 and press ENTER The following display appears and the test begins Enter Diag test 3 CHILLER TEST 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
50. com Setting Up PCR Programs and Methods Introduction This chapter describes how to use the HOLD CYCL and AUTO programs to create your own PCR programs You will learn how to store access edit and print these programs This chapter also describes how to setup 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setting Hold Times on the GeneAmp PCR System 9600 5 2 If you have used the DNA Thermal Cycler or DNA Thermal Cycler 480 read the following information on setting hold times These general guidelines are based upon differences in how the instruments heat and cool samples The hold times that you specify in your PCR Cycle and Auto programs for the GeneAmp PCR System 9600 will be shorter than those you used for your Step Cycle or Thermo Cycle files on the DNA Thermal Cycler This is because the DNA Thermal Cycler starts counting the hold 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
51. cord with a different style plug call an Applied Biosystems Service Representative Proper Location Place the GeneAmp PCR System 9600 on 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 Donotplace 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 excessively damp area Do not place the instrument in a Cold Room i e a refrigerated room The GeneAmp PCR System 9600 operates most efficiently when the ambient temperature is 15 to 30 degrees C 59 to 86 degrees Fahrenheit and the ambient relative humidity is 20 to 80 Do not operate in an environment where there is an oil mist 2 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setting Up the Printer The GeneAmp PCR System 9600 can be used with an optional Epson LX 810 printer or other Epson compatible printers with a serial RS 232C interface board The printer is shipped with an Epson C82302 serial adapter card when ordered as part of Printer Kits N801 0313 for 115VAC operation or N801 0314 for 230VAC operation The card must be installed in the printer as instructed in pages 5 38 to 5 51 of the Epso
52. displays in 5 32 5 32 hold for a specific time interval 4 9 in PCR method 4 14 last display in 5 32 run time displays 6 19 6 19 turning beeper on 5 32 types of 4 8 Hold time default value in HOLD program 5 32 definition of 3 4 setting in AUTO program 5 40 setting in CYCL program 5 34 Hold times converting from DNA Thermal Cycler for down ramps 5 6 5 7 for up ramps 5 4 5 5 default value in AUTO program 5 40 default value in CYCL program 5 34 in DNA Thermal Cycler 5 2 in GeneAmp PCR System 9600 5 2 HOME option description of 5 9 use in methods 5 17 Hot indicator light 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 chiller tests 2 19 2 21 parts supplied 2 2 power requirements 2 4 2 5 precautions 2 5 proper location of instrument 2 5 setting up a printer 2 6 2 13 115VAC printer 2 6 2 13 230VAC printer 2 10 2 13 unpacking 2 2 Internet address Documents on Demand S 19 K Keypad 1 4 4 2 description of 4 2 4 3 types of keys 4 3 L Laboratory requirements 2 5 Link files display 5 18 Lo
53. in temperature required to reach the next target temperature See Table 5 1 Ifyou are using a down ramp you will base the new hold time on the starting temperature of the ramp and the change in temperature 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 recommended hold time is 10 to 15 seconds for denaturation Table 5 1 After Up Ramps Converting Hold Times Greater than One Minute DNA Thermal Cycler to GeneAmp PCR System 9600 ATemp Seconds to Subtract from DNA Thermal C Cycler Hold Times gt 1 min 10 38 sec 15 45 sec 20 49 sec 30 54 sec 40 55 sec 50 57 sec 60 57 sec Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Figure 5 2 shows an example of converted hold times In this example the temperature was increased by 17 degrees C This value was rounded to 15 degrees C According to Table 5 1 we should subtract 45 seconds from the hold time on the DNA Thermal Cycler giving us a new hold time of 35 seconds DNA Thermal Cycler GeneAmp PCR System 9600 Temp Temp C C 72 72 A
54. instrument power loss Chapter 10 Specifications Lists and describes instrument specifications Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com If You Have Used the Applied Biosystems DNA Thermal Cycler or DNA Thermal Cycler 480 You will find that the GeneAmp PCR System 9600 is in many ways similar 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 Sample Block Sample Tubes CAUTION Do not use mineral oil or glycerine in the sample block of the GeneAmp PCR System 9600 The GeneAmp PCR System 9600 is designed for oil free operation The MicroAmp Reaction Tubes fit tightly in the wells and a heated cover exerts an even pressure on all tubes Mineral oil is not used on the sample surface because the heated cover eliminates condensation in the 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 Tra
55. of Instrument WARNING Hot Surface Use care when working around this area to avoid being burned by hot components AVERTISSEMENT Surface chaude WARNING Toreduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour r duire le risque de chocs lectriques ne pas ouvrir les couvercies si un outil est n cessaire Ne contient aucune pi ce pouvant tre r par e par l utilisateur Confier le d pannage au personnel qualifi de Applied Biosystems Left Side of Instrument WARNING For protection against fire hazard replace only with same type and rating of fuse AVERTISSEMENT Afin d assurer la protection contre les risques d incendie remplacer uniquement par un fusible de m me type et de m me courant nominal s4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Back of Instrument WARNING Grounding circuit continuity is vital for safe operation of equipment Never operate equipment with grounding conductor disconnected AVERTISSEMENT Risque de choc lectrique Pour un fonctionnement sans danger Ne jamais utiliser l quipment si le fil de terre n est pas raccord WARNING To avoid electrical shock disconnect power cord before servicing AVERTISSEMENT Pour viter les chocs
56. off and the run time beeper on or off These parameters appear together on one display If you have a printer setting the run time printer mode to ON lets you print run time data When the run time beeper is 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 Configuration EDIT PRINT 2 Press ENTER then press STEP The following display appears Runtime printer OFF Runtime beeper ON 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 The default condition of the run time beeper is on To turn the beeper off press OPTION ON 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 7 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Changing the Pause Time Out Limit The pause time out limit is the maximum amount of time a program can pause before it automatically aborts it applies only to the keypad pause The default value is 10 minutes This means that if you do not
57. on or off pause time out limit idle state setpoint allowed setpoint error temperature interval that triggers the clock start sample tube time constants Editing the Configuration Parameters 7 16 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 Configuration function The sections that follow explain how to edit the individual configuration parameters Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Configuration EDIT PRINT Press to display the first configuration parameter Time HH MM Date MM DD YY Runtime printer OFF tep Runtime beeper ON moves you TEET forward to the Pause time out limit next display XX XX Allowed setpt error K Un ct IX AH ct o mh a H u o oa TA Le oz P H Bc rp H 5 Back x xC moves you to cs Es a Idle state setpoint parameter 25C top g returns you to the Special tube NO Configuration display Set MICRO tube time constants NO Set THIN tube time constants NO Figure 7 6 The Configuration function Artisan Technology Gr
58. sampile reaches target temperature Figure 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 Tables 1 and 2 show some guidelines for converting hold times for the DNA Thermal Cycler or DNA Thermal Cycler 480 to hold times for the GeneAmp PCR System 9600 The table you use will depend on whether you are using an up ramp the temperature is higher than that used in the previous segment or a down ramp the temperature is lower Ifyou are using an up ramp you will base the new hold time on the change in temperature required to reach the next target temperature See Table 1 If you are using a down ramp you will base the new hold time on the starting temperature of the ramp and the change in temperature 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 recommended hold time is 10 to 15 seconds for denaturation Table 1 After Up Ramps Converting Hold Times Greater than One Minute DNA Thermal Cycler to GeneAmp PCR System 9600 If your change in Subtract this tim
59. temp Hold Hold 17 round 55 55 to 159 80 sec 35 sec Time Time 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 5 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 6 Table 5 2 After Down Ramps Converting Hold Times Greater than One Minute DNA Thermal Cycler to GeneAmp PCR System 9600 For down 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 based on the starting temperature of the ramp determine the number 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 gt 1 min ATemp 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 sec 30 56 sec 59 sec 40 57 sec 62 sec 50 62 sec 60 60 sec Figure 5 3 shows an example of converted hold times Artisan Technology Group Quality Instrumentation Guaranteed 888
60. temperature cycle the third PCR setpoint is commonly 72 degrees C and is held for 30 seconds Press STEP to accept the default ramp time temperature and hold time for Setpoint 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The following display appears Total cycles 25 Pause during run NO 6 Press the BACK key to review the display for Setpoint 3 The illustration below shows you how the BACK key works Setpt 3 Ramp 0 00 72 0C Hold 0 30 To display the previous screen Press Total cycles 25 Pause during run No 7 Now press STEP to move forward again to the next display Total cycles 25 Pause during run NO Total cycles specifies the number of times the three temperature cycle 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 3 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 12 8 Press STEP to accept the default values in the display The following display appears CYCL xx xC RUN STORE PRINT HOME This is the last display in the program From here you have the option of running storing or printing the program or reviewing it again In the next procedure you will go through th
61. temperature over a series of cycles Another use of an AUTO program is to incrementally increase the annealing temperature over the first several cycles for greater specificity of primer binding After the first several cycles usually two to five the annealing temperature is kept constant Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Extension Extension Extension Setpoint 3 Setpoint 3 Setpoint 3 94 72 Temp af ig oaa Cycle 1 Cycle 2 Cycle 3 Time Figure 4 7 An AUTO program used to increase hold time 4 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com PCR Methods PCR methods are used to automatically link together up to 17 programs for a specific PCR application To create a method you use the METH program An example of a method is shown in Figure 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 HOLD CYCL HOLD program program program 5 30 7 Denature Anneal Cycle 30 Cycle 1 Time min Figure 4 8 An example of a PCR method 4 14 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg
62. the sample tube caps MicroAmp Retainer 2 Press in the tabs on the front and back of the retainer fo MicroAmp release the tray Sample Tray Figure 6 6 Removing samples from the tray 6 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Specifying a Program or Method To specify the time and temperature pattern you want to use to run PCR samples you can create a new program or method edit an existing one or recall one you have previously stored Create a new program or method Select the CREATE option on the main menu and choose a type of program HOLD CYCL or AUTO Modify the parameters in the program displays by referring to the description of each program in Chapter 4 You can then immediately run the program or store 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 immediately run it or store it for later use then run it at any time Recall a stored program or method 6 10 Select the RUN option on the main menu to run a program or method that you have already set up and stored Artisan Technology
63. use the Edit function You can also modify an existing program to create a new one This can save you time when you need to change only certain program parameters To edit a program 1 Access the main menu Select Option 9600 RUN CREATE EDIT UTIL 2 Press the OPTION key to select EDIT then press ENTER You obtain the following display Edit Enter program 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 5 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 14 Note If you enter a number for a program that does not exist you will see a message that reads Program not found The next display allows you to choose the program number you want to edit again 4 Edit the program as necessary The displays in each program are described in the tables at the end of this chapter Press ENTER after you make a numeric entry Press STEP to advance to the next display Press BACK to return to a previous parameter or display 5 The last display gives you the option of storing the program Press the OPTION key to select STORE then press ENTER The following display appears Store Enter Program x The next available number x appears at the cursor 6 To store the program you have t
64. www artisantg com 7 8 For example if your first HOLD program is HOLD 14 the following display appears HOLD 14 4 Press STEP to view the next display in your program listing In our example the next HOLD program is HOLD 26 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Directory HOLD CYCL AUTO METH to move to the previous display HOLD 26 to return to the y first display Press HOLD 31 to move forward to the next display to return to the first display to return to the first display Figure 7 3 Example of a list of programs listed according to program type 7 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Listing Programs by their User Number USER 7 10 The USER selection lets you list all programs that have been stored under a previously specified user number While storing a program you have the option of protecting the program by entering a user identification number This type of directory will also list the program type and program number To list your programs by their u
65. www artisantg com The HOLD Program During a HOLD program the temperature of the sample block and the sample is held at one temperature for either a fixed time interval or an indefinite 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 Hold at 4 0C Hold FOREVER forward to the next display Beep While Hold NO 10 00 BACK moves you fo Back the previous display or parameter STEP moves you HOLD xXx C RUN STORE PRINT HOME STEP returns you to the first disolay Figure 5 8 The series of displays in a HOLD program 5 31 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hold at 4 0C Hold FOREVER 10 00 Beep While Hold NO HOLD xx xC RUN STORE PRINT HOME 5 32 Description of HOLD Program Displays This display allows you to set the temperature at which the sample will be held and the length of time this temperature will be maintained Press ENTER to accept the default temperature 4 degrees C or select a different temperature Enter the temperature in a decimal form but do not type the decimal point For example to specify 82 0 degrees C press 8 2 0 Then press ENTER For the hold time press ENTER to accept the default va
66. xx xC When the temperature of the block cover is within ten degrees of the sample block temperature the following display appears Wait 3 minutes Time MM SS B1lk 95 0C This displays shows the current sample block temperature BIk 95 0C and a clock which counts up from zero in minutes and seconds Time MM SS Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com When the clock reaches three minutes the following display appears Record Temperature Time MM SS B1k 95 0C 13 Measure the temperature of well E1 using the digital thermometer and record this temperature as T 95 Note To exit the test at any time press the STOP key Press 5 and ENTER to return to the Verify Calibration Diagnostic test Figure 8 3 shows when you should take the two measurements 3 Clock starts ae Measure well E1 40 T 95 Measure well E1 T 40 Time Figure 8 3 Temperature measurements in the temperature calibration verification test 8 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Test Results Perform the following steps to calculate the results of the test You will need to refer to the calibration label that you pasted into Figure 8 4 below for the High and Low Offset values PASTE THE CALIBRATION LABEL HERE Figure 8 4 GeneAmp PCR System 9600 Calibration Label Note If you hav
67. you want then find the document you want and record the index number Use the index number when requesting documents following the procedures below by phone for fax delivery From the U S or Canada call 1 800 487 6809 or from outside the U S and Canada call 1 858 712 0317 Follow the voice instructions to order the documents you want Note There is a limit 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 Under Resource Libraries click the type of document you want Enter or select the requested information in the displayed form then click Search In the displayed search results select a check box for the method of delivery for each document that matches your criteria then click Deliver Selected Documents Now or click the PDF icon for the document to download it immediately Fillin the information form if you have not previously done so then click Deliver Selected Documents Now to submit your order Note There is a limit of five documents per request for fax delivery but no limit on the number of documents you can order for e mail delivery Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com S 19 rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE
68. 0 Calibration Label 8 10 The probe assembly in sample wells A1 and A2 8 14 Measurements in the temperature uniformity test 8 15 Location of wells used in uniformity test 8 16 Removing the fuses 8 18 Sample temperature overshoot after ramping up 10 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Preface Using the Manual The GeneAmp PCR System 9600 is a highly sophisticated yet easy to use temperature cycling instrument designed specifically to automate the PCR technique Using the Manual The main function of this manual is to give you all the information needed to operate the GeneAmp PCR System 9600 in as productive a way as possible 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 Reference Guide Applied Biosystems Part No 0993 8690 Artisan Technology Group Quality Instrumentation Guaranteed 888
69. 00 542 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 Outside North America Telephone Fax Region Dial Dial Africa and the Middle East Africa English Speaking and West Asia Fairlands South Africa 27 11 478 0411 27 11 478 0349 South Africa Johannesburg 27 11 478 0411 27 11 478 0349 Middle Eastern Countries and North Africa Monza Italia 39 0 39 8389 481 39 0 39 8389 493 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Telephone Fax Region Dial Dial Eastern Asia China Oceania Australia Scoresby 61 3 9730 8600 61 3 9730 8799 Victoria China Beijing 86 10 64106608 86 10 64106617 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2593 6470 6471 822593 6472 Malaysia Petaling Jaya 60 3 758 8268 60 3 754 9043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 2358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 75 0 43 0 1 867 35 75 11 Belgium 32 0 2 712 5555 32 0 2 712 5516 Czech Republic and Slovakia Praha 420 2 61 222 164 420 2 61 222 168 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 3
70. 22 See also Running programs summary of steps 6 1 Run time beeper turning on and off 7 20 Run time display in CYCL program 3 26 6 78 use of the MORE key 3 26 3 26 6 18 Run time displays in CYCL and AUTO programs 6 17 in CYCL program 6 17 in HOLD program 6 19 Index 8 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Run time displays 6 17 6 19 Run time keys 4 3 6 11 Run time printer mode turning on and off 7 20 turning on 2 13 S Sample block cover cleaning 8 3 use in sample tray installation 6 6 use in trial run 3 23 use of cover knob 6 7 Sample block temperature idle state setpoint 7 25 in chiller test 7 53 in heater test 7 51 in temperature calibration verification test 8 7 range of 10 3 uniformity of 10 3 Sample block 1 3 and target temperature 5 2 general description of 1 3 1 4 numbering of wells in 6 2 Sample compartment 10 1 sample tubes 10 1 Sample temperature 5 2 accuracy of 10 3 allowed setpoint error 7 23 displayed 10 3 in CYCL program 5 33 in HOLD program 5 31 overshoot 10 3 10 4 setting in AUTO program 5 40 setting in CYCL program 5 34 setting in HOLD program 5 32 testing uniformity of 8 13 verifying calibration of 8 4 8 12 Sample tray 96 position 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
71. 3 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 48 22 866 40 10 48 22 866 40 20 and Estonia Warszawa Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Russia Moskva 7 095 935 8888 7 095 564 8787 South East Europe Zagreb Croatia 385 1 34 91 927 385 1 34 91 840 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 1206 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d IJssel 31 0 180 331400 31 0 180 331409 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com S 17 Telephone Fax Region Dial Dial United Kingdom 44 0 1925 825650 44 0 1925 282502 Warrington Cheshire All other countries not 44 0 1925 282481 44 0 1925 282509 listed Warrington UK Japan Japan Hacchobori Chuo 8135566 6230 81 3 5566 6507 Ku Tokyo Latin America 305 670 4350 305 670 4349 Del A Obregon Mexico To Reach We strongly encourage you to visit our Web site for answers to Technical Support frequently
72. 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 8 4 To create a program you need to select the CREATE option Press the OPTION key once to move the cursor under CREATE Select Option 9600 RUN CREATE EDIT UTIL Cursor 5 Press ENTER The next display appears You have now learned how to make a menu selection Using the OPTION key you mark your selection then you press ENTER to accept it You ll do this again in the next step Create program HOLD CYCL AUTO METH 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 3 Temperature PCR Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com A Look at the CYCL Program In the following steps you will look at the main displays in the CYCL program In each display you will see the default parameters e g times and temperatures that make up a common PCR cycle Using the STEP key you will quickly step through all the displays and accept the default values Keep in mind however that default values can be changed which you will do later on in this tutorial 1 The first screen in the CYCL program should still be on your display 3 Temperature PCR Cursor This display sets the number of setpoints or incubat
73. 88 SOURCE www artisantg com P 2 We recommend that you follow this approach to learn about the GeneAmp PCR System 9600 1 Read this chapter to learn about the conventions used in the manual Read Chapter 1 to familiarize yourself with the instrument hardware and software If you are installing the instrument yourself use this chapter as a guide Use the tutorial in Chapter 3 to learn the basic operation of the system in about 30 minutes When you have completed the tutorial go through Chapters 4 and 5 to learn more about the software and setting up PCR programs and methods 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 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 diagnostics and maintain your directory of programs Chapter 8 contains maintenance procedures Chapter 9 explains how to solve some basic instrument problems and when to call service Chapter 10 lists and describes instrument specifications Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Conventions The following conventions are used in this manual Software Conventions The instrument display is pictured as follows
74. C and the Low Offset printed on your calibration label is 0 1 then you would use the following formula for computing the block average at 40 C Block Average at 40 C 39 9 0 1 39 8 C In this example since 39 8 C does not differ by 0 75 C from your programmed target temperature your instrument would not need to be recalibrated 3 Remove the probe assembly from the sample block and move the digital thermometer ON OFF RANGE switch to the OFF position 8 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 8 12 4 Clean the oil from wells D1 and E1 using cotton 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 Temperature Uniformity Test Use this procedure to test the temperature uniformity of the sample block in the GeneAmp PCR System 9600 Equipment Required You will need the following equipment Temperature Verification System Testing the Temperature Uniformity Perform the procedure as described in the following steps 1 If the heated cover is in the forward position turn the cover knob completely counterclockwise then slide the cover back Coat all the wells in sample block rows A C E and H with mineral oil u
75. CL 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 cycle Linking Programs in a PCR Method You may also create a Method which links together up to 17 programs For example a method could include a HOLD file used for pre PCR incubation followed by a three temperature CYCL program followed by a final HOLD program for post PCR incubation 4 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Time Figure 4 3 HOLD CYCL AUTO and METH programs Storing Programs and Methods By storing the programs and methods you can 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 4 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The HOLD Program During a HOLD program the temperature of the sample block and the sample is held at one temperature for either a fixed time interval or an indefinite period Figures 4 4 and 4 5 show the two common types of HOLD programs A HOLD program would normally be used before or after runn
76. E www artisantg com Note If you enter a program number for a program that does not exist you will see a message that reads Program not found The next display allows you to choose the program number you want to edit again A program can appear more than one time in a method Also the same program can be used in more than one method 5 Press STEP to move to the next display If you are linking seven or more programs 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 Meth 25 6C RUN STORE PRINT HOME This display allows you to run store or print the method In most cases you will want to store the method so that it can be run at any time Instructions for storing a method are given on page 5 21 5 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 20 8 The last display to appear when you are creating a method allows you to run store or print the method Program Type Method METH xx xC RUN STORE PRINT HOME Program Number not yet assigned 9 In most 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 me
77. ENTER 10 Press STOP to return to the Utilities menu Press STOP again to return to the main menu 2 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Configuring the GeneAmp PCR System 9600 The final procedure in installing the GeneAmp PCR System 9600 is checking the instrument configuration The configuration parameters include time and date run time printer mode on or off run time beeper on or off pause time out limit allowed setpoint error idle state setpoint temperature interval that triggers 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 Select function DIR CONFIG DIAG DEL 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 instructions see Chapter 7 Utilities 2 14 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Summary of Configuration Parameters Configuration This display lets you edit or print the configuration EDIT PRINT parameters Press ENTER to select EDIT The first configuration screen used to set the time and date is displayed Time HH MM Set
78. ENTER to store the method under the displayed number OR To use a different number type the number 1 150 then press ENTER The following display appears Store Protect program NO 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 5 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 12 If you select YES the following display will appear Store Enter user _ In this display you can specify any number from 1 to 9999 for your user identification number Make a note of the number you choose for later use Type the number then press ENTER The following display appears Prog x User xxxx OK to store YES Note If 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Editing a Program When you want to view a program you have stored or make changes to it you
79. Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Power Failure xxx x hrs This message is also a fatal error message and will appear if a power failure 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 for this time and at this temperature Figure 7 9 shows an example status record display for a successful run Program Type Program Method Record Time of Abort CYCL 2 7 5 Abort 12 21 90 14 47 Status Message Date of Abort Figure 7 9 A typical status record display The example in the figure tells you that CYCL program 2 which is one of the linked programs specified in Method 7 was aborted at 14 47 2 47 PM on December 21 1990 and that this status record is Record 5 of your entire run 7 41 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Data Records in a History File As mentioned earlier a data record contains all pertinent numerical data about a run Every program has at least one data record A simple HOLD program for example
80. IDE Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com S 7 WARNING Grounding circuit continuity is vital for safe operation of equipment Never operate equipment with grounding conductor disconnected AVERTISSEMENT Risque de choc lectrique Pour un fonctionnement sans danger Ne jamais utiliser l quipment si le fil de terre n est pas raccord WARNING To avoid electrical shock disconnect power cord before servicing AVERTISSEMENT Pour viter les chocs lectriques d brancher le cordon d alimentation avant le d pannage CAUTIONThis unit contains protective circuitry Contact Applied Biosystems service before performing any AC line tests AVERTISSEMENT Cet appareil contient des circuits de protection V rifier aupr s de Applied Biosystems avant d effectuer des essais de secteur BACK VIEW Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Electrical Safety Testing CAUTION Routine safety testing of analytical instruments e g high potential voltage testing may be required by various safety agencies Testing should only be carried out by qualified personnel after seeking advice from the Applied Biosystems Service Department Internal AC line surge suppressors may need to be disconnected before a test is performed On completion of the tests it is essential to reconne
81. Keys SE 2s ue eee cad he Dies Reese 5 8 Example of a printout fora CYCL program 5 16 Example of a method printout using METHOD 5 26 Example of a method printout using PROGRAM DATA 5 27 The series of displays ina HOLD program 5 31 The main displays in a three temperature CYCL program 5 33 The main displays in a three temperature AUTO program 5 39 Setting up the 96 position sample tray 6 3 Securing the retainer on the tray 6 4 Placing the sample tray in the block 6 5 Sliding the heated cover forward 6 6 Turning the cover knob 6 7 Removing samples from the tray 6 9 Run Time KeyS see ss ste 5524568 SoS eeeew sed ee wes Gens 6 11 An example printout of a CYCL program using the SETPOINT option 226232v e2eececoseesteasasdseescsese 6 15 Run time displays fora CYCL program 6 17 Using the MORE key se0ciscssdugeedseesds bveeeedeeneus 6 18 More run time information ina CYCL program 6 18 Run time displays for a HOLD program 6 19 Example history file printout of a CYCL program 6 22 The Utilities functions 7 3 Example of a list of programs listed according to program number 7 6 Example of a list of program
82. PCR samples 3 27 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Software Basics Introduction This chapter presents an overview of the GeneAmp PCR System 9600 software and describes the HOLD CYCL 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 OH PCR Methods Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Reviewing Keypad Basics If you haven t already done so go through the Tutorial in Chapter 3 to learn how to use the keys The following section summarizes the functions of the keys On the left side 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 Run More Back Step Pause Option 7 Stop Enter Figure 4 1 Keypad 42 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Use of the Keys Run
83. RCE www artisantg com Printing a Program If the instrument is configured for a printer you can obtain a printout of the parameters in a program For more information on configuring a printer see Chapter 7 Utilities 1 You can print any program when the last display in the program is on the screen The last display for the Cycle program is shown below To quickly get to this display while you are in a program press STOP CYCL xx xC RUN STORE PRINT HOME 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 printout for a CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Creating and Editing Methods The main steps involved in creating and editing methods are summarized below These steps are explained in more detail on the following pages 1 Start at the main menu 2 Choose one of the following a Onthe main menu select CREATE if you want to create a new method b Then select METH on the next display OR a Select EDIT on the main menu if you want to view or edit a method you have already stored an
84. Replacement Parts 2 3 Power Requirements 2 4 Proper Location 2 5 Temperature Humidity and Environment 2 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 3 Setting Up the Printer ssiiacumascumadishensit hentenit 2 6 Installing the 115 VAC Printer 2 6 Installing the 230 VAC Printer 2 10 Configuring the Printer 2 12 Configuring the GeneAmp PCR System 9600 2 14 Summary of Configuration Parameters 2 15 Heater and Chiller Tests 2 19 Heater TeSt 2524 seh se cceodeetiepieseeeageeescesaes 2 19 Chiller TS i 6449603 CRG sae se SESE Se bok TERRE RO Paes 2 21 Tutorial Customizing a PCR CYCL Program 3 1 IMIGUUCION c2acd22552e82egeeesee dentiste 3 1 Before You STAR ses nee 5ee eee koe SE Eee boos CERT ORO pan KER 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 th CYCL Program 2 sus orssaiveerd ssemtobss 3 9 Customizing the CYCL Program 3 14 Defining the Number of Setpoints 3 14 Defining Values for Setpoint 1
85. Setpt 1 Hrs left 0 5 Prog Tot Cyc 30 1 Figure 6 10 Using the MORE key The parameters in the second run time display are explained in Figure 6 11 Current setpoint Total cycles in program Setpt 1 Tot Cyc 25 Hrs left 1 2 Prog 26 Estimated time left in Program program Figure 6 11 More run time information in a CYCL program Press MORE again to return you to the first run time display The MORE key toggles between the two run time displays 6 18 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com HOLD Program Run Time Display Figure 6 12 shows the run time displays for a HOLD program Use the MORE key to view the second run time display Press the MORE key again to return to the first run time display Current sample Programmed target temperature temperature xx xC Prog 1 Hold at 95 0C 4 30 Time remaining Current program To move between the two run time displays Hrs left 0 2 Prog 1 Figure 6 12 Run time displays for a HOLD program Time remaining Current program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 6 19 Pausing a Run Stopping a Run 6 20 Once a run has started you can manually pause a run in order to add a reagent to your samples for example using the PAUSE key Note that the instrument will automatically pause i
86. TO Program 220 5 4ssese0seeanae aa areas Raed 5 39 The Displays in an AUTO Program 5 39 Description of AUTO Program Displays 5 40 Running PCR Samples 6 1 Introduction s csar nated share etais ENERE Ri 6 1 Loading Samples 2322 40 SUR AMAR SANS SN RASE 6 2 Using the 96 Position Sample Tray with MicroAmp Reaction TUDES ari essere e E E E E E ae aie 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 Recall a stored program or method 6 10 Starting the Run 2222 2445 dete evdegeeeed daa seaprabiverd 6 11 RUN KEYS a uon a ae anana drama nt diinea des 6 11 Running a Stored Program 6 12 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 7 Indicator LIGNIS 22 4405 222 taeee SoS es ew SEs SS oe RSS 6 16 Run Time DISplaysS 2axs cde hommes Fa ee awiawes banked 6 17 CYCL and AUTO Program Run Time Displays 6 17 HOLD Program Run Time Display 6 19 Pa
87. accepting selections 3 8 function of 5 8 Entering whole numbers 3 15 ERROR history file display option 7 45 7 47 Error messages in history file 7 43 ERRORS history file print option 7 48 F Files See Programs 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 installation 2 19 pass fail display 7 57 Heating and cooling rate 10 4 Heating indicator light 6 16 Heating ramps on System 9600 and DNA Thermal Cycler 5 3 Heating samples See Sample temperature Help See Technical support S 14 High offset 8 10 History file description of 6 22 display options 7 45 example CYCL program printout 6 22 PRINT HISTORY display 7 47 printing 7 48 printout of all records in 7 49 records in 7 38 viewing all records in 7 46 Index 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com viewing data records with error messages in 7 47 viewing status records in 7 47 viewing 7 44 7 47 HOLD program defining values in 5 32 definition of 4 8 description of 4 8 4 9 5 32
88. ace 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 in the tray so leave the cover knob fully counterclockwise This keeps the plate raised above the tray since no samples will be heated 3 22 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Side View With the cover knob counter Full counterclockwise clockwise the plate is raised up position from the block Figure 3 5 Sliding the heated cover forward for a trial run Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 23 Running the Program 3 24 1 Look at the display The main menu shown below should be displayed If not press the STOP key one or two times Select Option 9600 RUN CREATE EDIT UTIL 2 With the cursor beneath RUN press ENTER The following display appears Run Enter program _ 3 Press the key for the number of the program you created and stored earlier in this tutorial If it was the first program stored on the system press 1 Then press the ENTER key The following display appears Select tube MICRO Reaction vol 100uL 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 Ifthe printer has been enabled using the Utilit
89. ading a sample tray 96 position tray 6 2 6 8 without samples 3 22 Loading samples 6 2 6 4 Low offset 8 11 Index 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com M Main menu 3 6 CREATE option description of 4 4 cursor on 3 6 description of 3 6 4 4 4 5 EDIT option description of 4 4 getting to the 4 4 options on 4 4 4 5 RUN option description of 4 4 selecting a function on 4 5 4 6 selecting options on 3 7 3 7 using the STOP key to return to 5 29 UTIL option description of 4 4 Maintenance procedures 8 1 8 18 cleaning the sample block cover 8 3 cleaning the sample wells 8 2 temperature calibration verification test 8 4 8 12 temperature uniformity test 8 13 Messages in history file status records 7 40 METH program description of 4 14 selecting on main menu 5 18 Method Program See METH program Methods creating and editing 5 17 5 27 summary of steps 5 17 creating 5 18 5 20 definition 5 18 editing 5 23 5 25 example 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
90. are three types of programs stored in instrument memory abbreviated as the HOLD CYCL and AUTO programs Each program contains a thermal profile in which values can be entered to fit your specific temperature control application Programs can be linked together in a PCR method to accommodate complete amplification experiments 1 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 1 6 The software lets you create store and modify your own customized time and temperature programs and protect these programs with a user number if desired link several programs together to create and store a PCR method automatically 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 Guaranteed 888 88 SOURCE www artisantg com Installing the GeneAmp PCR System 9600 Introduction This chapter describes how to install the GeneAmp PCR System 9600 If your instrument has already been installed by an Applied Biosystems Service Representative disregard these instructions The following sections are included in this chapter
91. at the program doesn t have a program 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 3 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Storing Your CYCL Program 1 The following display should appear on your screen CYCL xx xC RUN STORE PRINT HOME 2 Press the OPTION key to move the cursor beneath STORE then press ENTER The following display appears Store Enter program x At the cursor x is the next available program number If this is the first program stored on the instrument x would be a 1 on the display 3 Press ENTER to store the program under the displayed number The following display appears Store Protect program NO 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 3 20 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The following display appears Prog x OK to store YES 5 Press ENTER to store the program The following display appears Program Type Assigned Program Number 1 CYCL CYCL 1 xx xC RUN STORE PRINT HOME O
92. ature 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 2 10 5 Temperature Calibration 10 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Illustrations Figure 1 1 Figure 1 2 Figure 1 3 Figure 2 1 Figure 2 2 Figure 3 1 Figure 3 2 Figure 3 3 Figure 3 4 Figure 3 5 Figure 4 1 Figure 4 2 Figure 4 3 Figure 4 4 Figure 4 5 Figure 4 6 Figure 4 7 Figure 4 8 Figure 5 1 The GeneAmp PCR System 9600 1 1 Sample block and heated cover 1 3 The control Panel 022024 bei edi bee eee esas Goveateserda es 1 4 DIP switch Settings on the Epson C82302 serial interface card 2 8 Side panel of the GeneAmp PCR System 9600 and rear panel of the printer showing DIP switch settings and cable CONNECTIONS ended se oasis thee ee dente crane os a 2 9 A common CYCL program 3 3 Setting temperature and time values for Setpo
93. bes 3 Use the roller end of the tool to press a row of caps into a row of sample tubes Using moderate force roll the tool along a single row of caps pressing the caps into the tubes The roller 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 instrument 1 Make sure the sample block is not hot the Hot indicator light is not on 2 Turn the cover knob completely counterclockwise then slide the heated cover back 3 Grasp the sample tray retainer assembly firmly with both hands and gently rock it back and forth until the tubes are free 6 8 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Removing Samples from the Tray The following procedure describes how to remove the sample tubes from the tray 1 Place the sample tray back on the base and remove the sample caps Remove the tray from the base 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 Remove
94. ce of the sample block which may be hotter than 100 degrees Celsius See Chapter 7 for cleaning instructions Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Instrument Cover CAUTION This unit contains protective circuitry Contact Applied Biosystems before performing any AC line tests WARNING To reduce the chance of electrical shock do not remove covers that require tool access There are no user serviceable components inside the instrument Refer servicing to Applied Biosystems qualified service personnel Temperature Humidity and Environment CAUTION This instrument is designed for 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 instrument is able to withstand transient overvoltage according to Installation Category II as defined in IEC 1010 1 CSA 1010 1 and UL 3101 1 S 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Storage Conditions Electrical Warnings S 12 Pollution Degree This equipment will operate safely in envir
95. chnology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com If you have a printer and it has been enabled using the Configuration function the following display appears Select print mode OFF CYCLE SETPOINT This display lets you select the type of printout you want 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 program 7 Press the OPTION key to choose one of these print options When the cursor is under your desired option press ENTER The following display appears Close and tighten the sample cover Make sure the heated cover is closed and tightened down After a few seconds the run starts 6 14 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com AB GeneAmp PCR System 9600 Ver 2 Tube type MICRO Reaction vol 100uL Start CYCL Program 3 Setpt Setpt Cycle Setpt Setpt Cycle Setpt Setpt Cycle Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 1 2 1 1 2 2 1 2 3 RAMP HOLD RAMP HOLD Program Program Program Program Complete RAMP HOLD RAMP HOLD Program Pro
96. ct CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER then press STEP three times The following display appears Allowed setpt error 2 0C 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 you 7 23 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 24 4 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 Entering an Idle State Setpoint Value The idle state setpoint is the temperature of the block when a program is not running the idling temperature The Configuration function lets you change the idle state setpoint value The default value for the idle state setpoint is 25 degrees C The instrument will automatically heat or cool to this temperature while idling and the Heating light on the control panel will flash To edit this configuration parameter 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT Press ENTER then pr
97. ct 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 Regulations based on Section 15 103 c S 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Operating Precautions Sample Block Cover S 10 This manual contains important information regarding potential hazards that may arise during the operation of the instrument It is essential that this information is read and thoroughly understood by all potential users of the instrument This section describes precautions that must be observed in order to assure safe operation If used otherwise the protections provided by the instrument can be impaired CAUTION To protect your samples and to guarantee 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 sample block WARNING During routine operation do not lift the heated cover This will expose the surfa
98. d assigned a number Link together a series of programs 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 print the list of linked programs or the program parameters for each program HOME Select this option to display the main menu 5 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Creating a Method 5 18 A method is a series of up to 17 programs linked together For example you can link a HOLD program to a CYCL program and conclude your experiment with another HOLD program To create a method Access the main menu Select Option 9600 RUN CREATE EDIT UTIL Press the OPTION key to select CREATE then press ENTER You obtain the following display Create program HOLD CYCL AUTO METH Press the OPTION key to select METH then press ENTER The following display appears Link progs _ 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 Link progs 1 3 5 o Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURC
99. e GeneAmp PCR System 9600 operates on one of the following input voltages Maximum Operating Voltage Freq Current Part No volts Hz amps Power watts N801 0001 120 60 10 850 N801 0002 230 240 50 5 850 220 50 5 850 N801 0003 100 50 12 850 100 60 12 850 For 220 volt operation with instrument Part No N801 0002 a conversion kit is required and included Applied Biosystems Part No N801 0110 For 60 Hertz operation with instrument 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 2 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com All 230VAC instruments are wired for single ended line service 230VAC instruments installed in locations that have double ended line service or locations that have unpolarized power receptacles as in Germany must be rewired using the instructions provided with the 230V to 220V Conversion Kit Applied Biosystems Part No N801 0110 The 220 230 VAC units are supplied with a power cord that has a Continental European style plug also known as Schuko or CEE 7 7 f you need a power
100. e from your temperature C is Thermal Cycler hold time 10 38 sec 15 45 sec 20 49 sec 30 54 sec 40 55 sec 50 57 sec 60 57 sec Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Note If methods developed on the GeneAmp PCR System 9600 are to be used on the DNA Thermal Cycler you can use Table 1 to convert the hold times from GeneAmp PCR System 9600 to DNA Thermal Cycler Simply add the indicated times instead of subtracting them For down 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 based on the starting temperature of the ramp determine the number 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 Table 2 After Down Ramps Converting Hold Times Greater than One Minute DNA Thermal Cycler to GeneAmp PCR System 9600 If your change in Subtract this time from the DNA temperature C is Thermal Cycler hold time if the starting temperature of the ramp is 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 sec 30 56 sec 59 sec 40 57 sec 62 sec 50 62 sec 60 60 sec Note If methods developed on the GeneAmp PCR System 9600 are to be used on the DNA Th
101. e 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 8 10 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Ifthe block average is more than 0 75 degree C above or below 95 degrees C your instrument must be recalibrated For example If the measured temperature of well E1 at was 95 2 C and the High Offset printed on your calibration label is 0 1 then you would use the following formula Block Average at 95 C 95 2 0 1 95 3 C In this example since 95 3 C does not differ by 0 75 C from your programmed target temperature your instrument would not need to be recalibrated Note The offsetis the number of degrees Celsius that the temperature of well E1 differed from the average temperature of the block when the instrument was calibrated at the factory 2 Use the following formula to calculate the average block temperature at the 40 degree C hold Block Average at 40 C T 40 Low Offset Ifthe 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
102. e program again to customize it with new PCR parameters 9 Press STEP to return to the first display 3 Temperature PCR 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 Temperature PCR STEP moves you BACK moves you fo forward to the Step Baek the previous disolay next disolay Step Back or parameter Setpt 1 Ramp 0 00 94 0C Hold 0 30 Setpt 2 Ramp 0 00 55 0C Hold 0 30 Setpt 3 Ramp 0 72 0C Hold 0 30 Total cycles 25 Pause during run NO STEP returns you to the first display levee CYCL xx xC Step RUN STORE PRINT HOME Figure 3 4 Moving through the CYCL program displays 3 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Customizing the CYCL Program In the steps below you will customize the CYCL program by changing some of the default parameters Although we suggest some new temperatures and times to use you may want to choose values relating to a current PCR application in your lab Defining the Number of Setpoints 3 14 1 The first display in the CYCL program shown below should appear on your display If it does not press STOP one or two times to return to the main menu
103. each cycle amplification through 25 cycles would theoretically yield a 33 million fold increase of specific product The PCR method readily lends itself to research applications Cloning of the amplified sequence can be facilitated by extending the 5 end of the primers with short sequences harboring Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com restriction sites Dideoxy sequencing can also be performed on the amplified product Instrument Description The GeneAmp PCR System 9600 contains a programmable heating and cooling block which rapidly and uniformly heats and cools PCR samples A Look at the Sample Block The sample block is a 96 well aluminum block Up to 96 samples in MicroAmp Reaction Tubes 0 2 mL are loaded in a sample tray and placed in 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 Sample Block Heated Cover 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 responsible for rapid heating and control of the sample block The heater is designed so that 1 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www arti
104. eater 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 10 of temperature uniformity test 8 17 Thin walled GeneAmp reaction tubes changing the time constant 7 32 7 34 Time constant See Sample tube time constant Time See Hold time Ramp time Tray See Sample tray Troubleshooting table 9 2 9 4 Troubleshooting 9 1 9 5 Tube type See Sample tube type Tubes See Sample tubes Tutorial 3 1 3 27 about the 3 1 before you start 3 2 customizing a CYCL program 3 14 3 19 getting to the CYCL program 3 6 3 8 running a program 3 24 3 27 starting a trial run 3 22 3 27 storing a CYCL program 3 20 3 21 viewing displays in CYCL program 3 9 3 13 Two temperature CYCL program creating 3 27 TYPE on directory display 7 7 Index 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com U by user number 7 10 7 12 7 12 Viewing the history file 7 44 7 47 Unpacking the instrument 2 2 Unprotected programs deleting 7 61 W User diagnostics See Diagnostic tests 9 g WWW address User identification number See User Applied Biosystems S 18 numbers Documents on Demand S 19 User numbers 5 12 use in deleting programs 7 59 7 60 use in storing methods 5 22 use in storing programs 5 11 viewing a directory of programs list
105. echnology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 60 The following display will appear showing in which method the program is linked Can t delete file xxx Linked in method xxx The number xxx on the top line of the display pictured above represents the program number of the program that cannot be deleted 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 User xxxx Delete all progs YES 6 Press ENTER to delete the files Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Deleting All Unprotected Programs You can delete any program provided that it is not linked ina method or protected under a user number To delete all unprotected programs 1 Select DEL on the Utilities menu as described on page 7 3 The following display appears Delete PROGRAM USER ALL 2 Press the OPTION key twice to move the cursor to ALL then press ENTER The following display appears Delete every unprotected prog YES 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 7 61 Artisan Technology Group Quality Instrumenta
106. ed by 7 10 7 12 USER on directory display 7 10 7 12 UTIL option on the main menu 4 4 Utilities menu accessing 7 2 functions on 7 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 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 type 7 7 7 9 7 9 Index 12 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales Offices Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For international office locations please call our local office or refer to our web site at www appliedbiosystems com www appliedbiosystems com AS Applied gt Biosystems Applera Corporation is committed to providing the world s leading technology and information for life
107. ems and MicroAmp are registered trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries Epson is a trademark of Seiko Epson Corporation AmpliTaq AmpliType GeneAmplimer AmpliWax EnviroAmp and Twelve Paq AmpliTaq are registered trademarks of Roche Molecular Systems Inc GeneAmp is a registered trademark of Roche Molecular Systems Inc Registered trademarks etc used in this document even when not specifically marked as such are protected by law Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Safety and Regulatory Information Conventions Used in This Manual WARNING A warning indicates an operation that could cause 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 S 1 Symbols and Conventions Used on the Instrument There are three different types of warning symbols that appear on the instrument This symbol indicates an operation or condition on the A instrument that could cause personal injury or instrument damage if precautions are not followed This can be any type of hazard When you see this symbol refer to the safety pages
108. er Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Printing a Directory of Your Programs PRINT The PRINT selection of the Directory function lets you print a directory of your programs organized by program number PROG program type TYPE or user number USER To print a directory 1 Select DIR on the Utilities menu as described on page 7 3 The Directory display appears Directory PROG TYPE USER PRINT Press OPTION three times to move the cursor to PRINT then press ENTER The following display appears Directory Print PROG TYPE USER 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 7 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 14 Directory Print Enter program If the above display is shown type the program of the first program in the directory you want to print then press ENTER All your programs will be printed beginning with the program you entered Directory Print HOLD CYCL AUTO METH If the above display is shown press the OPTION key to move the cursor to the program type of which you want to print a directory then press ENTER For example if you select HOLD
109. er files On the DNA Thermal Cycler the run time display counts down the number of cycles On the GeneAmp PCR System 9600 the run time display counts up the number of cycles To pause a run on the DNA Thermal Cycler press the STOP key once On the GeneAmp PCR System 9600 use the PAUSE key to pause a run or you can specify an automatic pause in your CYCL or AUTO program On the DNA Thermal Cycler an auto tuning diagnostic test checks instrument operation With the DNA Thermal Cycler 480 and the GeneAmp PCR System 9600 no auto tuning 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 controlled in the idle state This parameter is called the idle state setpoint and you can program it by selecting UTIL on the Main menu then selecting CONFIG The default value is 25 degrees C When the block is at this temperature the Heating light on the control panel flashes When a run has been completed on the DNA Thermal Cycler SHUT OFF appears on the display When a run has been completed on the GeneAmp PCR System 9600 DONE appears on the display Artisan Technology Group Quality
110. erature values in successive cycles 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 used to add or remove sample tubes during a run Press the OPTION key to change the NO response default to a YES and vice versa When the desired response is displayed press ENTER 5 43 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Pause after setpt 1 Beep while pause YES lst pause at cyc 1 Pause every 25 cyc s Pause time 10 00 5 44 The display appears only if you specified a pause in the previous display In this display you define the setpoint after which you want to pause the run Type the number of the desired setpoint then press ENTER During the pause you specify whether or not you want a beeper to sound Press the OPTION key to change the YES default to a NO and vice versa When the de sired response is displayed press ENTER This display only appears if you specified a pause during the run In this display you specify the number of the cycle in which you want the run to pause The default value 1 indicates that the instrument will pause during the first cycle after the specified setpoint P
111. ermal 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents Preface Chapter 1 Chapter 2 Using the Manual 63 5 c50545 066505 00008505000 s se eseeeetes P 1 Using th Manual asasan aana beak Bee de be Keeberabaes P 1 CONVENIONS 1m dass dar is ratios bien P 3 Software Conventions P 3 Notes and Warnings P 4 Introducing the GeneAmp PCR System 9600 1 1 Introduction 13322 434 ad oa ee ed Ba eae ee 1 1 Principles of Operation 22422 eee asta spa bes be aan ans 1 2 Instrument Description 1 3 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 Installing the GeneAmp PCR System 9600 2 1 Introduction 2 2 1 Unpacking sis ses oni na CES ens eee ew ethan OLS Rad die oe hs 2 2 Pals Supplied 124 c2ccugesdecenteteetesderh eens bhe554 2 2 Supplies Accessories and
112. es 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setpt 2 Ramp 0 00 55 0C Hold 0 30 You can accept any of the default values for Setpoint 1 by pressing the ENTER key or you can change the values using the following steps 1 Forthe ramp time use the numeric keys to specify the time in minutes and seconds For example to specify a ramp time of one minute press 1 0 0 then press ENTER 2 For the setpoint temperature enter the temperature in decimal form You do not type a decimal point For example to specify 96 0 degrees C press 9 6 0 then press ENTER 3 Specify the hold time in minutes and seconds then 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 shown in the display to the left You can accept any of the default values for Setpoint 2 by pressi
113. ess STEP four times The following display appears Idle state setpoint 25C 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 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 7 25 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Changing the Temperature Interval for the Setpoint Clock 7 26 Whenever you run a program there is an interval before the setpoint temperature is attained The clock starts counting the hold time at the beginning of this interval For example if the setpoint temperature is 95 degrees C and the temperature interval is 1 degree C the clock will actually start counting at 94 degrees C Figure 7 7 illustrates this example Setpoint Tem Setpoint clock starts here perature 1 C Interval 95 C o 95 C 94 C 94 C Sample Temperature C Time 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 foll
114. essed 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 Guaranteed 888 88 SOURCE www artisantg com Creating and Editing Programs The main steps involved in creating and editing programs are summarized below These steps are explained in detail in the following pages 1 Start at the main menu 2 Choose one of the following a Select CREATE on the main menu if you want to create a new program b On the next display choose the type of program HOLD CYCL or AUTO you want to create OR a Select EDIT on the main menu if you want to view or edit a program you have already stored and assigned a program number 3 View the displays in the program and make any changes to the thermal cycling parameters 4 Inthe 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 customized before running it Once you have stored a program it may be run at any time PRINT Select this option to print the program you have customized HOME Select this option to display the main menu 5 9 Artisan Technology Group Quality Instrumentati
115. f you select the Pause option in a CYCL or AUTO program WARNING Be careful not to touch the sample block or the bottom of the heated cover during a pause These 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 CYCL 26 xx xC PAUSE 10 00 This display occurs in a CYCL program Press RUN to resume the run from where you left off To abort a run at any time press the STOP key The following appears on the second line of the display Abort program YES If you want to abort the run press ENTER to accept the YES selection OR Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Press the STOP key again The run is aborted and a display similar to the one shown below appears CYCL 26 Abort xx xC RUN STORE PRINT HOME This display occurs in a CYCL program 3 If 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 Torun the program from the beginning select the RUN option 6 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Reviewing the History of the Run Once a run has been completed or aborted you can obtain a record of the run called a History file If you want to view t
116. function for example a directory or listing of your programs Select Option 9600 RUN CREATE EDIT UTIL Main menu Select function DIR CONFIG DIAG DEL Run Enter program From here you select one of the From here you can enter a Utilities functions program number and start a run Edit Enter program Create Program HOLD CYCL AUTO METH From here you select the type of From here you enter the number program you want fo create or of the program you want to edit select METH to create a method Figure 4 2 Access to the major functions of the software 4 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com An Overview of PCR Programs and Methods A program is a set of instructions in which you specify how the instrument should heat and cool your samples for PCR Three types of programs are stored in the instrument software HOLD CYCL and AUTO You can view each program by scrolling through a series of displays on the front panel screen Each program contains default parameters which you can change as necessary to customize the program Think of a program as similar to a form which you can fill out with your thermal cycling instructions The three types of programs are described below AHOLD program consists of a single temperature held for a specific time interval or for an extended e g overnight period ACY
117. gram Program Program Complete RAMP HOLD RAMP HOLD Progran Program Program Program Complete 94 94 68 68 34 94 68 68 94 94 68 68 Run Complete Figure 6 8 An example printout of a CYCL program using the SETPOINT option June 1 1992 clock within 1 0C of setpt oc 0 00 oc 0 30 oc 0 00 oc 0 30 oc 0 00 oc 0 30 oc 0 00 oc 0 30 oc 0 00 oc 0 30 oc 0 00 oc 0 30 June 1 Actual Actual Actual Actual Actual Actual Actual Actual Actual Actual Actual Actual 93 94 69 67 93 94 69 67 93 94 69 67 1992 11 31 am oc 1C oc 9C oc ic oc 9C oc 1C oc sc O0 0Om OOOO O O0 00 24 30 2 22 30 41 30 2 22 30 41 30 22 30 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 11 24 am 6 15 Indicator Lights The three indicator lights on the control panel of the instrument indicate the operating status as described below Heating when lit indicates that the heater is active When flashing it indicates that the system is controlling the 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
118. grams by 7 4 7 6 7 6 Programming a pause in AUTO program 5 43 in CYCL program 5 36 Programs creating 5 10 definition of 1 5 4 6 editing 5 13 5 15 linking in methods 4 6 4 7 overview of 4 6 4 7 overwriting 5 15 printing 5 16 5 17 recalling 5 30 5 31 running 6 1 6 22 storing 5 11 5 12 5 14 types of 1 5 4 6 4 7 Protected methods 5 25 Protecting programs 5 11 R Ramp time repeatability 10 4 Ramp time defining in CYCL porgram 5 34 definition of 3 4 Reaction volume 7 29 Recalling programs 5 30 5 31 Removing samples 6 9 Removing the sample tray 6 8 Retainer See Sample tray retainer Reviewing the history file 7 38 7 49 See also History file data records 7 42 status 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 Tutorial 3 24 3 27 pausing a run 6 20 RUN option 6 12 run time displays 6 17 6 19 runtime keys 6 11 selecting a print mode 6 14 selecting sample tube type 6 12 6 13 specifying a program 6 10 starting a run 6 11 stopping a run 6 20 stored programs 6 12 Running samples 6 1 6
119. has only one data record Data records include the following information record number ending setpoint temperature cycle number except in HOLD programs setpoint 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 an error message in place of the program type and program number 7 42 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Any one of the following error messages can appear on a data record display Setp Error This message will appear if the setpoint was not reached in a reasonable period 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 Figure 7 10 shows an example of a data record display for successful run 7 43 Artisan Tech
120. he current History file for a run you must view it before you start the next run since each time a new run begins the previous History file is erased A History file can contain status records or data records Status records 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 to use the diagnostic tests AB GeneAmp PCR System 9600 Ver 2 June 1 1992 12 00 pm History File Rec Program Status Temp Time Cyc Setpt 1 CYCL 3 Tube type is MICRO 2 CYCL 3 Reaction volume is i00uL 3 CYCL 3 Start clock within 1 0C of setpoint 4 CYCL 3 Run Start June 1 1992 11 24 am 5 CYCL 3 94 1C 1 54 1 1 6 CYCL 3 67 9C 0 52 1 2 7 CYCL 3 9 4 1C 1 11 2 1 8 CYCL 3 67 9C 0 52 2 2 9 CYCL 3 94 1C 1 11 3 1 10 CYCL 3 67 9C 0 52 3 2 11 CYCL 3 Run Complete June 1 1992 11 31 am Figure 6 13 Example history file printout of a CYCL program 6 22 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Utilities Introduction This chapter explains the Utilities functions The Utilities functions let you display or print programs by thei
121. ies function a display that reads Select print mode appears Select OFF and press ENTER since a printer is not used in this example Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 Before the run starts a display will appear that reminds you to close and tighten the heated cover When the run starts you will see a run time display that is continuously updated for the program being run During ramp segments you will see the following display Setpoint temperature Current sample 7 y temperature Ramp to 96 5C xx xC 0 30 Cycle 1 Time remaining in current A Current cycle ramp or hold segment During hold segments you will see the following display Setpoint temperature Current sample y temperature Ramp to 96 5C xx xC 0 22 Cycle 1 Time remaining in current ramp or hold segment Current cycle These two run time 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Current setpoint number RE Total cycles in program O Setpt 1 Tot Cyc 30 Hrs left 0 7 Prog 1 Estimated time left in A program Current program 7 Press MORE again to return you to the first run time display The illustration below shows you ho
122. iguration display appears Press the STOP key to return to the Main menu Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Diagnostic Function DIAG The Diagnostic function gives you access to five different diagnostic tests These tests are review the most recent instrument run by examining the History file test the sample block heating system test the sample block cooling 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 Review History File Heater Test Chiller Test System Performance Test Verify Calibration TEST 1 2 3 4 5 7 35 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Selecting the Diagnostic Tests There are two ways to select a diagnostic test You can enter the number of the test you want to run or You can use the STEP key to scroll forward through the test displays and the BACK key to scroll backward through the test displays To select a diagnostic test by entering its test number 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears Enter Diag Test 1 Enter test REVIEW HISTORY FILE here 2
123. in the manual for further information AVERTISSEMENT 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 danger of electric shock if A precautions are not followed due to the presence of high voltage AVERTISSEMENT Risque de choc lectrique S 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Additional graphic symbols used on the instrument are the following Nw Indicates alternating current Indicates the primary protective grounding terminal C 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 S 3 Warnings on the Instrument The following sections present the warning labels affixed to the instrument 100 120 The following warning labels are affixed to the front the left side and 220 230 and the back of the instrument as shown in the figures on the Volt Models following pages for all three voltage models 100 120 and 220 230 Front
124. ineer will use the results to identify the instrument problem 7 Press STOP to return to the first Diagnostic display 7 55 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Running the Verify Calibration Test Diagnostic test 5 is the Verify Calibration test Run this test to verify that your instrument is still 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 7 56 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Delete Function DEL The Delete function lets you delete unprotected programs one by one by specifying their program numbers delete protected programs stored under a user number by specifying that user number and delete all unprotected programs In all cases 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 Delete PROGRAM USER ALL 2 With the cursor positioned under PROGRAM press ENTER 7 57 Artisan Technology Group
125. ing 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 48 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 100 Temp W C 7 0 Time Figure 4 4 A HOLD program held for an indefinite time 100 N 73 72 7 minutes Temp 71 o lt Hold Time 0 Clock Time Starts Figure 4 5 AHOLD program held for a specific time interval 4 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com CYCL The Cycle Program 4 10 A CYCL program contains the thermal ramp and hold segment patterns for PCR cycling It contains up to nine setpoints Each setpoint comprises a ramp segment and a hold segment for the specific target temperature The pattern can be repeated up to 99 times A complete cycle for a common profile requires about three or four minutes Typically there are two or three setpoints in a CYCL program The first setpoint is commonly used for DNA denaturation or melting For 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 pri
126. ing runtime printer mode on and off 7 20 7 21 use of keys in 7 16 Configuration parameters 7 16 See also Configuration function editing 7 16 7 17 in installation 2 14 2 16 printing 7 34 summary of 2 15 2 18 Control panel 10 2 display 10 2 general description of 1 4 1 4 indicator 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 16 summary of steps 5 9 Creating methods summary of steps 5 17 Customer support See Technical support CYCL program creating a two temperature 3 27 defining number of cycles in 5 36 defining the number of setpoints in 5 34 defining the number of setpoints 3 14 defining values for Setpoint 1 3 15 5 34 defining values for Setpoint 2 3 17 5 35 defining values for Setpoint 3 3 17 5 36 definition of 4 10 description of 3 3 3 3 4 10 4 11 5 33 5 38 displays in 3 13 5 33 5 34 5 38 example printout 5 16 example SETPOINT printout 6 15 first display in 3 8 hold times in 3 4 in PCR method 4 14 in temperature uniformity test 8 14 last display 3 19 5 38 parameters of 4 11 progra
127. int 1 3 4 Location of power switch 3 5 Moving through the CYCL program displays 3 13 Sliding the heated cover forward for a trial run 3 23 Keypad 4525 ces eee iranien rieur kas 4 2 Access to the major functions of the software 4 5 HOLD CYCL AUTO and METH programs 4 7 HOLD program held for an indefinite time 4 9 HOLD program held for a specific time interval 4 9 A common CYCL program 4 11 An AUTO program used to increase hold time 4 13 An example of a PCR method 4 14 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 5 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Figure 5 2 Figure 5 3 Figure 5 4 Figure 5 5 Figure 5 6 Figure 5 7 Figure 5 8 Figure 5 9 Figure 5 10 Figure 6 1 Figure 6 2 Figure 6 3 Figure 6 4 Figure 6 5 Figure 6 6 Figure 6 7 Figure 6 8 Figure 6 9 Figure 6 10 Figure 6 11 Figure 6 12 Figure 6 13 Figure 7 1 Figure 7 2 Figure 7 3 Sample conversion of hold times for up ramps DNA Thermal Cycler to GeneAmp PCR System 9600 5 5 Sample conversion of hold times for down ramps DNA Thermal Cycler to GeneAmp PCR System 9600 5 7 Editing
128. ion 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 Template Denaturation Setpt 1 Ramp 0 0 0 LE 94 0C Hold 0 30 Hold 94 en yi f This display sets the ramp time temperature and hold time for Temp Setpoint 1 typically used for template denaturation oC Ramp The temperature of the first PCR setpoint is 94 degrees C and is held for 30 seconds Time 3 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Primer Annealing Temp Le 55 Setpoint 2 Ramp Hold Time Primer Extension Temp 3 10 72 Setpoint 3 Hold Ramp Time Press STEP to accept all of the default values and move to the next display The display for Setpoint 2 appears Setpt 2 Ramp 0 00 55 0C Hold 0 30 This display sets the ramp time temperature and hold time for Setpoint 2 used for primer annealing For a three temperature cycle the second PCR setpoint is commonly 55 degrees C and is held for 30 seconds Press STEP to accept the default ramp time temperature and hold time for Setpoint 2 The display for Setpoint 3 appears Setpt 3 Ramp 0 00 72 0C Hold 0 30 This display sets the ramp time temperature and hold time for Setpoint 3 used for primer extension For a three
129. ise then slide the heated cover back Move the probe assembly to wells A4 and A5 with the dummy probe in A5 N Slide the heated cover 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 BODOM0008000 000000000000 Front of instrument l Probe Dummy Probe Dummy Probe Dummy Probe Probe Probe Probe Figure 8 7 Location of wells used in uniformity test Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Test Results 14 15 When you have completed all measurements remove the probe assembly from the sample block and turn off the digital thermometer Clean the oil from the sample block For the 16 Setpoint 1 measurements 95 C hold subtract the lowest measured temperature from the highest measured temperature 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 888 88 SOURCE www artisantg com 8 17 Changing
130. ity Instrumentation Guaranteed 888 88 SOURCE www artisantg com Principles of Operation 1 2 The GeneAmp PCR System 9600 automates the Polymerase Chain Reaction PCR technique for amplifying DNA The Polymerase Chain Reaction PCR technique is conceptually a very simple method for amplifying nucleic acids It mimics the natural DNA replication process in that the number of DNA molecules generated by the Polymerase Chain Reaction doubles after each cycle In the PCR technique the typical cycle consists of three steps Denaturing the template DNA by heating it to a high temperature 94 degrees C to 95 degrees C thereby producing two single strands of DNA Annealing of the target specific primers to the two separated DNA strands by cooling the reaction mixture to a lower temperature 37 degrees C to 65 degrees C Extending the annealed 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 of the reaction will be discrete double stranded DNA molecules whose termini will be determined by the set of primers used Because the copy number of the target DNA doubles after
131. logy Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Selecting a Utilities Function To select one of the Utilities functions 1 Press OPTION to move the cursor from one function to the next When the cursor reaches DEL press OPTION to move the cursor back to DIR 2 When the cursor is under your desired selection press ENTER You will then see the first display for the function you selected Figure 7 1 shows the first displays for the Utilities functions Select function DIR CONFIG DIAG DEL Directory Delete PROG TYPE USER PRINT PROGRAM USER ALL The Directory function lets you display The Delete function lets you or print programs by their program delete individual programs by their program number their type or their user number and user number or delete all number programs Enter Diag Test 1 REVIEW History file Configuration EDIT PRINT The Configuration function lets you The Diagnostic function lets you configure and set default values for review recent instrument runs general instrument operating and perform heater chiller system parameters performance and calibration verification tests Figure 7 1 The Utilities functions 7 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Directory Function DIR The Directory function lets you display or print programs according to program
132. lows 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER then press STEP until the following display appears Set THIN tube time constants NO 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 Press ENTER If your instrument has software version 1 05 or higher the following display appears Rxn vol 100uL T 12 0 Rxn vol 50uL T 12 0 If your instrument has software version 1 04 or lower the following display appears Rxn vol 100uL T 14 6 Rxn vol 50uL T 14 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com These displays let you change the sample tube time constant There are two default values for sample tube time constants on this display one for sample tubes with a reaction volume of 100 uL and one for sample tubes with a reaction volume of 50 uL There is a time constant default value for sample tubes with a reaction volume of 20 uL that appears on a separate display If your instrument has software version 1 05 or higher press STEP to view the following display Rxn vol 20uL T 12 0 If your instrument has software version 1 04 or lower press STEP to view the following display Rxn vol 20uL T 14
133. lue of 10 00 minutes or use the numeric keys to change to the hold time then press ENTER For an infinite soak press the OPTION key The cursor moves to FOREVER and the default time changes to 0 00 minutes You 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 display in the program indicates the program type followed by which means that the program has not yet been stored and assigned a number It also displays the calculated sample temperature In the second line of the display the options allow you to run store or print the program or return to the main menu Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com CYCL The Cycle Program A CYCL program contains the thermal ramp and hold segment patterns for PCR cycling It contains up to nine setpoints Each setpoint comprises a ramp segment and a hold segment for the specific target temperature 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
134. m Performance test 7 54 7 55 available options 7 55 getting to 7 54 viewing the results of 7 55 Index 10 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com T Target temperature See also Sample temperature Setpoints in CYCL programs 3 4 See also Sample temperature Technical support S 14 S 19 E mail address S 14 Internet address S 18 Telephone fax S 15 S 18 Temperature calibration specification 10 5 Temperature calibration verification test 8 4 8 12 See also Verify calibration test calculating results of 8 10 8 12 equipment required 8 4 first measurement in 8 8 measurements in 8 9 placing probe in sample wells 8 6 sample block temperature in 8 7 sample wells used in 8 5 second measurement in 8 9 use of Diagnostic Test 5 8 7 Temperature interval See Setpoint clock Temperature range 10 3 Temperature uniformity test sample wells used in 8 16 Temperature uniformity test 8 13 8 17 calculating results of 8 17 equipment required 8 13 first measurement in 8 15 measurements in 8 15 8 16 placing probe in sample wells 8 14 procedure 8 13 8 17 sample wells used in 8 16 8 16 second 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 H
135. menu by pressing the STOP key until it is displayed Note Ifthe display on your screen has the following options RUN STORE PRINT HOME you can select HOME to get to the main menu Press the OPTION key to move the cursor under HOME then press ENTER The functions on the main menu are described below 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 anew 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 a history of the run review a list of your stored programs configure the GeneAmp PCR System 9600 run diagnostics or delete programs The Utilities functions are described in Chapter 7 44 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Selecting a Function 1 Press OPTION to move the cursor from one option to the next When the cursor reaches UTIL pressing OPTION again will move it back to RUN 2 When the cursor is at the desired selection press ENTER You will then see the first display 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
136. mer 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 points of the target sequence For the third setpoint the primers are extended For example DNA can be polymerized at approximately 72 degrees C fora time interval of typically not less than 15 seconds Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setot 1 Setpt 2 Setpt 3 Denature Anneal Extend 04 Hold 72 Temp 2C 55 E C Cycle 2 ycle 1 Time Figure 4 6 A common CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The AUTO Program 4 12 An AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every cycle By increasing the extension time with each cycle it may be possible to increase product yield with a fixed amount of enzyme The enzyme is not initially limiting but eventually if more enzyme is not added longer times may be needed to continue with exponential increases 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
137. method and save the old one see Step 6a Or you can replace the original method with the new version 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 Type the original number for the method then press ENTER This allows you to replace the original method with the new edited version The subsequent display will ask OK to overwrite Select YES and the original method will be overwritten by the new edited version Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com If the original method was protected you will need to enter the user identification number that was specified when the method was first created before you can overwrite the method The following display will appear Prog x is protected Enter user _ Type the correct user number then press ENTER The next display will ask OK to overwrite Select YES and the original method will be overwritten 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
138. mming a pause in 5 36 5 37 ramp times in 3 4 Index 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com setpoints in 3 3 4 10 5 33 specifying the number of cycles in 3 18 storing 3 20 target temperatures in 3 4 CYCLE print option 6 14 Cycle program See CYCL program Cycles defining total number in AUTO program 5 43 defining total number in CYCL program 5 36 D Data record display 7 44 error messages in 7 43 in a history file 7 42 7 44 information in 7 42 Decimal values entering 5 35 Default values definition of 3 4 See also HOLD program CYCL program AUTO program DEL function See Delete function Delete function 7 57 7 61 deleting all unprotected programs 7 61 deleting programs by program number 7 57 7 58 deleting programs by user number 7 59 7 60 description of 7 2 7 57 Deleting programs all unprotected programs 7 61 by program number 7 57 7 58 by user number 7 59 7 60 if linked in method 7 59 Denaturation See PCR technique DIAG function See Diagnostic tests Diagnostic function description 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
139. n In this display you specify how long the instrument should pause Specify the pause time in minutes and seconds then press ENTER 5 37 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com CYCL 7 xx xC RUN STORE PRINT HOME 5 38 The last display in the program indicates the program type followed by which means that the program has not 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The AUTO Program An AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every cycle The Displays in an AUTO Program 3 Temperature PCR Setpt 1 94 0C Hold for 0 30 Setpt 1 94 0C Change time temp NO Step Setpt 2 55 0C IDOVEE YOU Hold for 0 30 forward to the next display Setpt 2 55 0C Change time temp NO Back moves you to Setpt 3 72 0C the previous Hold for 0 30 display or parameter Setpt 3 72 0C Change time temp NO Total cycles 25 Pause during run NO AUTO 20 xx xC Press RUN STORE PRINT HOME Step to return to the first display Figure 5 10 The main displays in a three temperature AUTO program Artisan Techn
140. n LX 810 Instruction Manual as explained below Before installing the card set the DIP switches on the Epson C82302 card as described below The procedure for installing the printer is different for line voltages of 115 volts and 230 volts Follow the procedure given below for the line voltage you are using then configure 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 Setthe 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 described in pages 5 38 to 5 51 of the Epson LX 810 User s Manual When using this manual pay special attention to Removing the Upper Case on page 5 38 and Installing the Board starting on page 5 44 Note the figure 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 2 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 Connect one end of the cable Applied Biosystems Part No N801 0421 to the 25 pin D shell RS 232C connector on the side panel of
141. n this display CYCL is the type of program you have set up The number of the program appears on the display following the program type Your program is stored with the parameters you have entered From this display you could print the program parameters if a printer 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 Select Option 9600 RUN CREATE EDIT UTIL 3 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Starting a Trial Run In the following steps you will learn how to load a tray and run the program you just stored then stop it after a few moments You will not be loading any samples in the tray for this exercise but will be able to see how a run is initiated Loading a Tray without samples Load an empty tray in the sample block by following these steps 1 Turn the cover knob fully counterclockwise see Figure 3 5 This 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 Pl
142. ng hold times 5 2 5 7 Setting the time and date 2 13 7 18 7 19 Software basics of 4 1 4 14 features of 1 6 general description of 1 5 shortcuts 5 28 5 30 Specifications 10 1 10 5 control panel 10 2 display 10 2 indicator lights 10 2 keypad 10 2 displayed sample temperature 10 3 instrument dimensions 10 1 power requirements 10 2 printer interface 10 5 ramp time repeatability 10 4 sample block temperature range 10 3 sample block temperature uniformity 10 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 7 40 STEP key accepting default values 3 9 function of 5 8 moving to the next display 3 9 3 73 selecting diagnostic tests 7 36 use in directory function 7 5 STOP key function as runtime key 6 11 function of 5 8 shortcuts 5 28 5 29 Stopping a run 6 20 6 21 STORE option description of 5 9 selecting 5 11 use in methods 5 17 Storing a method 5 21 5 22 Storing a program 5 11 5 12 assigning a program number 5 11 entering user numbers 5 12 protecting programs 5 11 Storing methods 5 24 Syste
143. ng the ENTER key or you can change the values using the same procedure as that for Setpoint 1 see above 5 35 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setpt 3 Ramp 0 00 72 0C Hold 0 30 Setpt n Ramp 0 00 72 0C Hold 0 30 Total cycles 25 Pause during run NO Setpoint 3 in a typical cycle program is used for primer extension This display sets the ramp time target temperature and hold time for the third setpoint Setpt 3 The default values are shown in the display to the left You can accept any of the default values for Setpoint 3 by pressing the ENTER key or you can change the values using the same procedure as that for Setpoint 1 see above A display will appear for each setpoint up until the total number of setpoints specified in the first program display The default temperature for setpoints in CYCL programs with 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 used to add or remove sample tubes during a run Press the OPTION key to change the NO response default to a YES and vice versa
144. ng the Heater Test 7 50 Diagnostic Test 2 is the Heater Test which verifies the performance of the sample block heater and electronics by stabilizing the block temperature at 35 degrees C then applying full power to the heaters and measuring the temperature rise over a period of time CAUTION Before you begin this test make sure you place 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 To run the Heater Test 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears Enter Diag Test 1 REVIEW HISTORY FILE 2 Select Diagnostic Test 2 by pressing 2 then pressing ENTER or by pressing the STEP key The following display appears Enter Diag Test 2 HEATER TEST 3 Press ENTER to start the test Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The following display appears Heater Test Blk xx x going to 35C When the temperature stabilizes full power is applied to all heaters The display then reads ramping then timing and the block temperature is monitored When the block reaches the setpoint the following screen appears estes Test Passed This display will show Passed if the test was successful If
145. nology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Program Ending Setpoint Type Program Temperature CH 2 25 2C 6 Setpt 2 0 10 Record Elapsed Time Figure 7 10 A data record display of a CYCL run The above example tells you that this data record is record 6 of CYCL program 2 There is no method number because this program was not linked in a method This record also tells you that this is setpoint 2 of cycle 1 the ending setpoint temperature was 25 2 degrees C and the elapsed time was ten seconds If this were a data record for a HOLD program there would be no cycle number or setpoint 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 Enter Diag Test 1 REVIEW HISTORY FILE 2 Press ENTER to select Diagnostic Test 1 The following display appears History 7 recs ALL STAT ERROR PRINT Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The total number of records in the History file appears on the top line of this display In this example there are seven records in the History file On the bottom line there are four options ALL view all the records in the His
146. nter 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 local plug to the connector 230 VAC line power outlet 5 Plug the secondary line cord into the printer line cord receptacle located on the printer rear panel 6 Connect one end of the printer cable Applied Biosystems Part No N801 0421 to the serial port on the side panel of the GeneAmp PCR System 9600 and connect the other end to the serial adapter card you just installed Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Note When you are printing the printer ON LINE OFF LINE button must be in the ON LINE position 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 2 11 Configuring the Printer 1 Turn on the power switch located on the lower left side of the instrument A beeper sounds and all three indicator lights flash Two displays appear briefly Finally the instrument main menu appears Select Option 9600 RUN CREATE EDIT UTIL The cursor appears under the R in RUN 2 Press the OPTION key three times The cursor mo
147. number type or user identification number Once you view a directory you can return to Utilities menu or the Main menu using the STOP key Listing Programs by their Program Number PROG The PROG selection 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 Directory PROG TYPE USER PRINT 2 Press ENTER to select PROG The first display that you see prompts you to enter a program number Directory Enter program 1 7 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 Press the numeric keys that correspond to the program number of the program you want to list first then press ENTER In our example the default is shown Each of the next displays will list a program by its program number and type beginning with Program 1 4 Press STEP to view the next 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 CYCL 2 Press BACK to view the previous program in the list 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 comple
148. o move the cursor to DIAG then press ENTER The following display appears Enter Diag Test 1 REVIEW HISTORY FILE 10 Run the Verify Calibration Diagnostic Test Test 5 by pressing 5 then ENTER The temperature of the sample block and heated cover will go to 40 degrees C and the following display will appear Going to 40 C Cvr xxC Blk xx xC This display shows the current temperature of the 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 Wait 3 minutes Time MM SS B1lk 40 0C This displays shows the current sample block temperature BIk 40 0C and a clock which counts up from zero in minutes and seconds Time MM SS 8 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 8 8 When the clock reaches three minutes the following display appears Record Temperature Time MM SS Blk 40 0C 11 Measure the temperature of well E1 using the digital thermometer and record this temperature as T 40 See Figure 8 3 on the next page 12 Press ENTER The temperature of the sample block and heated cover will go to 95 degrees C and the following display will appear Going to 95 C Cvr xxC Blk xx xC This display shows the current temperatures of the block cover Cvr xxC and the sample block Blk
149. ology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 Temperature PCR Setpt 1 Hold for 5 40 94 0C 0 30 Description of AUTO Program Displays Defines the number of incubation temperatures or setpoints used in the PCR cycle A typical PCR cycle consists of three 3 setpoints therefore 3 is the default value Type the number of setpoints you wish in your DNA amplification experiment 1 9 then press ENTER This display sets the following values for the first setpoint Setpt 1 Setpoint temperature The 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 key or you can change the values using the following steps Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setpt 1 94 0C Change time temp NO 94 0C Delta T 0 0c Delta 0 00 1 For the setpoint temperature enter the temperature in decimal form You do not type a decimal point For example to specify 89 0 degrees C press 8 9 0 then press ENTER 2 Specify the hold time in minutes and seconds then pres
150. on Guaranteed 888 88 SOURCE www artisantg com Creating a Program 1 Access the main menu Select Option 9600 RUN CREATE EDIT UTIL 2 Press the OPTION key to select CREATE then press ENTER The following display appears Create a program HOLD CYCL AUTO METH 3 Press the OPTION key to select the type of program HOLD CYCL or AUTO you want to create then press ENTER The METH option is used to create a method See page 5 18 4 Specify the thermal cycling parameters for the program The displays in each program are described 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 Program Type Program Number not yet assigned CYCL CYCL xx xC RUN STORE PRINT HOME 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 5 10 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Storing the Program 1 Press the OPTION key to move the cursor beneath STORE then press ENTER The following display appears Store Enter program x The number x is the next available number If this is the first file being stored x would be a 1 on the display Up to 150 programs can be stored Press
151. on configuring a printer see Chapter 7 Utilities 1 You can print a method when the following display is shown METH xx xC RUN STORE PRINT HOME 2 Press the OPTION key twice to select PRINT then press ENTER The following display is shown Select option METHOD PROGRAM DATA 5 25 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 3 Select METHOD to print out a list of the linked program numbers specified in the method see Figure 5 6 Or select PROGRAM DATA to print out the complete program parameters for each program linked in the method AB GeneAmp PCR System 9600 Ver 2 June 1 1992 10 55 am METH Program HOLD Program 1 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 5 26 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com AB GeneAmp PCR System 9600 Ver 2 June 1 1992 10 59 am METH Program HOLD Program 1 Program Parameters Hold at 95 0C Hold for 5 00 Beep while Hold NO CYCL Program 2 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 To
152. on in this manual Read Chapter 1 in this manual Unwrap one of the MicroAmp Trays supplied with the instrument Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com What is a CYCL Program A CYCL program is a set of instructions in which you specify how the instrument should heat and cool your samples in a PCR cycle The CYCL program is stored in the instrument software You view the CYCL program by scrolling through a series of displays on the front panel screen By entering the times and temperatures for your 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 repeated up to 99 times Setot 1 1 Setpt 2 Setpt 3 Denature Anneal Extend Hold 55 i gt Cycle 2 ycle 1 Time Figure 3 1 A common CYCL program 3 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 94 Target Pai Temperature 3 4 For each setpoint you specify a target temperature a ramp time and a hold time see Figure 3 1 The ramp time is the time it takes to change from one
153. onments that contain nonconductive foreign matter up to Pollution Degree 2 in IEC 1010 1 CSA 1010 1 and UL 3101 1 The PCR 9600 may be stored under the following conditions ambient temperature is 20 to 60 C 4 to 140 F ambient relative humidity is 20 to 80 without condensation altitude is in the range 0 to 12 000 meters WARNING Connect the instrument to an AC line power outlet that 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 provided by the instrument WARNING Do not operate the instrument with any covers or parts removed WARNING Use only fuses with the required current rating and of the specified type for replacement Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Fuses and Power Interruption If power to the instrument fails or is turned off while the instrument is running turn the instrument off and wait five minutes before restarting If you 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 ins
154. oup Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setting the Time and Date 7 18 The Configuration function lets you set the time in hours and minutes and the date in months days and years To set the time and date 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER The following display appears Time HH MM Date MM DD YY 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 To set the date type in the appropriate numbers for the month day and year and 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 7 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Turning the Run Time Printer Mode and Run Time Beeper On or Off 7 20 The Configuration function lets you turn the run time printer mode on or
155. ove to the next display Total cycles 25 Pause during run NO 3 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Specifying the Number of Cycles Total cycles 25 Pause during run NO The first entry in the above display specifies the number of times the cycle will be repeated 1 Enter 30 cycles press 3 then press 0 When the entry is correct press ENTER The cursor moves to the entry Pause during run This allows you to pause a run to add a reagent to your sample solutions for example 2 The OPTION key is also used to change a NO selection to a YES and vice versa The illustration below shows how this function of the OPTION key works Total cycles 25 Pause during run NO Press To change NO to Total cycles 25 YES and vice versa Pause during run YES 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 3 18 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Program Type CYCL The next display the last display in the program is Program Number not yet assigned CYCLH xx xC RUN STORE PRINT HOME CYCL in this display means that the type of program you have set up is a CYCL program means th
156. owing display appears Configuration EDIT PRINT Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 Press ENTER then press STEP five times The following display appears Start clock within 1 0C of setpoint This example shows the default temperature interval of 1 degree C This means that the setpoint clock will start counting within 1 degree of the setpoint temperature 3 To enter a temperature interval different from the default value press the appropriate numeric keys then press ENTER The range of valid entries for the temperature interval is 0 5 to 1 0 degrees C If you decrease 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 parameter or press BACK to display the previous configuration parameter Press STOP to return to the first Configuration display 7 27 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Changing the Sample Tube Type 7 28 The Configuration function lets you specify a future sample tube type by defining the tube time constant characteristic
157. quipment Required 8 4 Verifying the Temperature Calibration 8 4 Test Results ais sxedesheseeegadagtentesgen satay gas 8 10 Temperature Uniformity Test 8 13 Equipment Required 8 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Chapter 9 Chapter 10 Index Testing the Temperature Uniformity 8 13 Test Results 8 17 Changing External Fuses 8 18 Troubleshooting 0cc00scesncceve ee stves sees beeveseees 9 1 Introduction 2 9 1 Troubleshooting 44 26 esse esse daebiiten detente 9 1 If the Instrument Turns Off 9 5 Specifications 4 ss sr ere enr ones ions 10 1 Dimensions 10 1 Sample Compartment 10 1 Sample Tubes 12514 dhs ci3enshes16d702iseshvadeaed 10 1 Power Requirements 10 2 Control PANG oi teak orca tae waa ale tne ee eae e eda de wanes 10 2 DEPlAVactccrhtatuaved he hedeenedoers terwendg eae ee 10 2 K yp d pe tecceueee hes ues este beuee oe em ewes es 10 2 Indicator LIQINS seit eue ne ed tee died ane se esate eee 10 2 Sample Temperature Range 10 3 Sample Temper
158. r and chiller tests as described in the following sections to verify that the instrument is operating correctly The heater test verifies that the sample block heaters and electronics are operating correctly At the conclusion of the test the display indicates whether the test was successful or not The test takes approximately three minutes to run CAUTION Before you begin this test make sure you place 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 STOP key until this display appears Select Option 9600 RUN CREATE EDIT UTIL 2 Press the OPTION key three times to move the cursor under UTIL then press ENTER The Utilities menu is displayed Select function DIR CONFIG DIAG DEL 2 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 20 3 Press the OPTION key twice to move the cursor under DIAG and press ENTER A display referring to the first diagnostic test appears Enter Diag test 1 REVIEW HISTORY FILE 4 Change the 1 to a 2 by pressing 2 Then press ENTER The following display appears and the test
159. r number their type or their user number see page 7 4 configure and set default values for 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting to the Utilities Menu 7 2 To get the Utilities menu 1 Getto the Main menu Press the STOP key once or twice until the Main menu appears Select Option 9600 RUN CREATE EDIT UTIL 2 Press the OPTION key three times to move the cursor to UTIL then press ENTER The Utilities menu appears Select function DIR CONFIG DIAG DEL The functions available from the Utilities menu are 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 programs as identified by program number and user number or delete all programs Artisan Techno
160. ranteed 888 88 SOURCE www artisantg com Chapter 8 THIN Time Constant 7 32 Printing the Configuration Parameters 7 34 The Diagnostic Function DIAG 7 35 Selecting the Diagnostic Tests 7 36 Reviewing the History file 7 38 About The History File 7 38 Status Records in a History File 7 39 Data Records in a History File 7 42 Displaying the History file 7 44 Printing the History file 7 48 Running the Heater Test 7 50 Running the Chiller Test 7 52 Running 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 Maintenance 2 05065 2st sid det eia sc te ences dk eeteeser teense 8 1 Introduction 25 soe ecko ede cee Oe Dee SERe Ties ee SUS ea eee iS 8 1 Cleaning the Sample Wells 8 2 Cleaning the Heated Cover 8 3 Temperature Calibration Verification Test 8 4 E
161. re may be changed to a new value For operator safety this value should be close to room temperature Press STEP to move to the next display Or press BACK to move to the previous display Enter the temperature interval before the setpoint temperature is reached at which the setpoint clock will start The default value 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 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 See Chapter 7 for details If you accept the default condition you will be able to select one of two sample tube types when you start a run MicroAmp Reaction Tubes or Thin Walled GeneAmp Reaction Tubes See Chapter 6 for more information Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com a To change the default condition press the OPTION key NO will change to YES on the display and you will be able to select a different tube type when you start a run see Chapter 6 for more information b Press ENTER The following display appears Rxn vol 100uL T 9 5 Rxn vol 50uL T 7 0
162. 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 samples to reach the target temperature A hold time of one minute or greater is required on the DNA Thermal Cycler for the samples to reach the target temperature On the GeneAmp PCR System 9600 hold times of less than one minute are generally used Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com DNA Thermal Cycler 480 Hold Time 94 93 Temp C Time Clock starts 1 minute when block reaches target temperature GeneAmp PCR System 9600 Hold Time 94 93 Temp C Time Clock starts when sample reaches target temperature Figure 5 1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 5 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 4 Tables 5 1 and 5 2 show guidelines on how to convert hold times for the DNA Thermal Cycler or DNA Thermal Cycler 480 to hold times for the GeneAmp PCR System 9600 The table you use will depend on whether you are using an up ramp the temperature is higher than in the previous segment or a down ramp the temperature is lower If you are using an up ramp you will base the new hold time on the change
163. ress 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 other cycle press 2 After you specify the number press ENTER This display only appears if you specified a pause during the run In this display you specify how long the instrument should pause Specify the pause time in minutes and seconds then press ENTER Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The last display in the program indicates the program type followed by which means that the program has not 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 5 45 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Running PCR Samples Introduction To run samples turn on the instrument and follow these procedures which are explained in this chapter
164. restart a run within 10 minutes after you pause it the run is aborted The Configuration function lets you change the pause time out limit To change the pause time out limit 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER then press STEP twice The following display appears Pause time out limit 10 00 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 least one minute 4 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 7 22 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Changing the Allowed Setpoint Error The allowed setpoint error is the number of degrees the actual sample temperature may vary from the setpoint before the reading is recorded in the history file as an error The default value is 2 0 degrees C The Configuration function lets you change the allowed setpoint error value To change the allowed setpoint error value 1 Sele
165. ront 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 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 thermometer 8 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Dummy Probe in DI Probe Assembly Probe in El L ww O40 i 0 0 O f 0O r Thread probe SD en wires through gt gt oic notch always faces front Figure 8 2 Placing the probe assembly into the sample wells 5 Slide the heated cover forward and turn the cover knob clockwise until the white mark on the cover knob is aligned with the white mark on the cover 6 Turn on the digital thermometer by moving the ON OFF RANGE switch to the 200 position 7 Turnonthe GeneAmp PCR System 9600 The main menu appears Select Option 9600 RUN CREATE EDIT UTIL 8 Press the OPTION key three times to move the cursor to UTIL then press ENTER The utilities menu appears 8 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Select function DIR CONFIG DIAG DEL 9 Press the OPTION key twice t
166. rtisantg com Printer Interface The GeneAmp PCR System 9600 uses an RS 232C serial port as its printer interface In addition the following 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 10 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Note A page number in italics e g 5 26 indicates an illustration A Aborting a run 6 20 6 21 ALL history file display option 7 45 7 46 ALL history file print option 7 48 typical printout 7 49 Allowed setpoint error changing 7 23 7 24 default value 7 23 definition of 7 23 AUTO program automatic incrementing and decrementing of setpoints 5 41 defining number of cycles in 5 43 defining the number of setpoints in 5 40 defining values for Setpoint 1 5 40 defining values for Setpoint 2 5 42 defining values for Setpoint 3 5 43 definition of 4 12 description of 4 12 4 13 4 13 5 39 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 di
167. ructions on how to set up and run a CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 8 On the third cycle measure the temperature of well A1 90 seconds into Setpoint 1 95 degrees C setpoint temperature using the digital thermometer The time remaining clock on the run time display will read 0 30 30 seconds Record this temperature 9 Still on the third cycle measure the temperature of well A1 90 seconds into Setpoint 2 40 degrees C setpoint temperature using the digital thermometer The time remaining clock on the run time display will read 0 30 30 seconds Record this temperature Figure 8 6 shows when to measure the temperatures Measure well A1 Measure well A4 90 seconds into Measure well Ai 90 seconds into Setpoint 1 Setpoint 1 90 seconds into N Setpoint 2 Measure well 95 A4 90 seconds into i Move Move the the 40 probe LM probe to well A4 to well A8 Cycle 3 lt a Cycle 4 Time 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 8 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 10 After you measure the second temperature of well A1 turn the cover knob completely counterclockw
168. run time printer mode configuration parameter is not turned on The printer has been in correctly set up Bad Printer cable Possible controller failure Check and or Remedy Review the history file to determine when the power failed Note that the system comes up in a 4 degree soak to save any samples The display shows how long power was interrupted Turn the run time printer mode on Check the printer set up Replace the printer cable Contact an Applied Biosystems Service Engineer Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com If the Instrument Turns Off If power is interrupted and the instrument turns off while you are operating it the following will occur when you turn it back on If you were editing a program you will lose the changes to that program and will have to re edit it The instrument 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 9 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation G
169. s Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Function Keys To do this On the DNA Thermal On the GeneAmp PCR Cycler System 9600 Begin a run Press START from the Select RUN on the main menu first display in the file enter the program number then press ENTER Access a file Press FILE press the Select EDIT on the main menu numeric key s corre enter the desired program sponding to the desired number then press ENTER file number then press ENTER Access the File Press FILE Then press Select UTIL on the main menu Directory ENTER Access the Press FILE Then press Select UTIL on the main menu Configuration and YES Diagnostic files Move the cursorto Press STEP Press STEP the next display or parameter Move the cursorto Press HELP Press BACK the previous dis play or parameter Toggle between Press HELP Press MORE two run time dis plays Move the cursorto Press NO Press OPTION the next selection Exit a file Press STOP Press STOP Pause a run Press STOP Press PAUSE Abort a run Press STOP twice Press STOP twice Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File Storage Operation With the GeneAmp PCR System 9600 you can store up to 150 programs A method is assigned a program number and is considered an individual program The Thermal Cycler stores up to 93 us
170. s We recommend not specifying a special tube type unless future sample tube types become available To change the sample tube type and sample tube time constant value 1 Select CONFIG on the Utilities menu as described on page 7 3 The following display appears Configuration EDIT PRINT 2 Press ENTER then press STEP six times The following display appears 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 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 sample tube types when you start a run MicroAmp Reaction Tubes or Thin Walled GeneAmp Reaction Tubes Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 To change the default condition press the OPTION key NO will change to YES on the display and you will be able to select a different tube type when you start a run see Chapter 5 for more information 5 Press ENTER The following display appears Rxn vol 100uL T 9 5 Rxn vol 50uL T 7 0 This display lets you change the sample tube time constant There are two default values for sample tube time constants on this display one for sample tubes with a reaction volume of 100 UL
171. s description of 5 9 in methods 5 25 in System Performance test 7 55 selecting 5 16 use in methods 5 17 Printer cable connection 2 7 Printer 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 10 Printer Kit 2 10 serial adapter card 2 10 use of 230V adapter 2 10 serial adapter card DIP switch settings 2 8 serial adapter cards 2 6 specifications 10 5 Printing a directory 7 13 7 15 selecting a directory 7 13 Printing configuration parameters 7 34 Printing methods 5 25 5 27 METHOD option 5 26 example printout 5 26 PROGRAM DATA option 5 26 example printout 5 27 Printing programs 5 16 Printing the history file 7 48 7 49 Probe tray use in temperature calibration verification test 8 5 Probe See RTD probe PROG on directory display 7 4 Program not stored display 5 28 Index 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Program numbers assigning to methods 5 21 assigning 5 11 use in creating methods 5 18 5 45 use in deleting programs 7 57 viewing a directory of pro
172. s ENTER For example to specify one minute and five seconds press 1 0 5 then press ENTER This display allows you to incrementally increase or decrease the hold time or temperature of the first setpoint in successive cycles Press the OPTION key to change the NO response default to a YES and vice versa This 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 arrow and vice versa This indicates whether you want a decrease or increase in the temperature 2 Press ENTER to move the cursor to the temperature entry Choose one of the following 5 41 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Enter the temperature increment in decimal form except you do not type a decimal point For example to specify a two degree increment press 2 then 0 Then press ENTER OR Press ENTER to accept the default 0 0 temperature This will not change the specified temperature of Setpoint 1 in successive cycles The cursor moves to the hold time increment 3 Press the OPTION key to change the arrow direction indicating whether yo
173. s listed according to program type 7 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Figure 7 4 Figure 7 5 Figure 7 6 Figure 7 7 Figure 7 8 Figure 7 9 Figure 7 10 Figure 7 11 Figure 7 12 Figure 7 13 Figure 8 1 Figure 8 2 Figure 8 3 Figure 8 4 Figure 8 5 Figure 8 6 Figure 8 7 Figure 8 8 Figure 10 1 Example of a list of programs listed according to user number 7 12 The PRINT selection of the Directory function 7 15 The Configuration function 7 17 Diagram of a 1 degree C temperature interval 7 26 Initial displays for the five diagnostic tests 7 37 A typical status record display 7 41 A data record display of a CYCL run 7 44 Viewing ALL the records in a History file for a two temper ature CYCL program 2x4 iii taient 7 46 Viewing the status STAT records data records with error messages ERROR and printing records PRINT 7 47 Printout of all status and data records ALL of a typical History files ER de phe eee es 2 eae Bees ee 7 49 Location of sample wells E1 and D1 8 5 Placing the probe assembly into the sample wells 8 6 Temperature measurements in the temperature calibration verification test 8 9 GeneAmp PCR System 960
174. santg com the power density at the edges is greater than that at the center to compensate for losses that may occur at the edges A Look at the Control Panel 1 4 The instrument control panel consists 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 Select Option 9600 RUN CREATE EDIT OTIL Cooling Stop Figure 1 3 The control panel Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Instrument Features Features of the GeneAmp PCR System 9600 include reproducibility of cycle times uniformity of PCR yields for samples sample tray accommodating up to 96 samples in an 8 x 12 format thin walled MicroAmp Reaction Tubes allowing efficient heat transfer and improving equilibration times high speed of heating and cooling so that more samples can be run in a fixed amount of time increasing productivity heated cover assuring that tubes fit tightly in the wells oil free operation The GeneAmp PCR System 9600 Software PCR time and temperature profiles are stored by the GeneAmp PCR System 9600 in programs program is a set of instructions that specify how the instrument should heat and cool your samples in a PCR cycle There
175. ser number 1 Select DIR on the Utilities menu as described on page 7 3 The Directory display appears Directory PROG TYPE USER PRINT 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 Directory Enter user 7777 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 stored under user 7777 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 Press STEP to view the next display In our example CYCL program 6 is listed CYCL 6 User 7777 5 Press STEP to view the next display which will list the next program stored under user 7777 In our example HOLD program 5 is listed HOLD 5 User 7777 Press BACK to view the previous program in the list 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 7 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 12 to return to the first display to move to the previous display to return to the first display Press to return to the first display Figure 7 4 Example of a list of programs listed according to user numb
176. sing a UM scsi 2a seas pen ye eh bee ae ee Res anus 6 20 Stopping a Run occ ccs an Gea eee esate epeehetkaees ae ets 6 20 Reviewing the History of the Run 6 22 Utilities esse entree Sea ee See aeeiese hes Sees enesis 7 1 INMOUOUCHOM EN 7 1 Getting to the Utilities Menu 7 2 Selecting a Utilities Function 7 3 The Directory Function DIR 7 4 Listing Programs by their Program Number PROG 7 4 Listing Programs by their Program Type TYPE 7 7 Listing 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 Onor Offeror a a Lan dan dns ee 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 Changing the Temperature Interval for the Setpoint Clock 7 26 Changing the Sample Tube Type 7 28 Setting Sample Tube Time Constants 7 30 MICRO Time Constant 7 30 Artisan Technology Group Quality Instrumentation Gua
177. sing a cotton swab 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 Place the probe assembly into wells A1 and A2 with the dummy probe in A2 Thread the probe wire through the notch in the probe tray see Figure 8 5 Make sure the probe is connected to the digital thermometer 8 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 8 14 Probe Assembly Probe in Al Not Dummy Probe in A2 Probe Tray Thread probe wires through me Notch notch always faces front Figure 8 5 The probe assembly in sample wells A1 and A2 5 Slide the heated cover forward and turn the cover knob clockwise until the white mark on the cover knob is aligned with the white mark 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 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 inst
178. splay 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 Cover See Sample block cover C Calibration See Temperature Calibration Verification test Calibration label 8 10 Caps See MicroAmp reaction tubes CE key clearing entries 3 15 function of 5 8 Chiller test 7 52 7 53 accessing 7 52 in installation 2 21 pass fail display 7 53 Cleaning sample wells 8 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Cleaning the sample block cover 8 3 Clear Entry key See CE key Condensation See Loading samples CONFIG function See Configuration function Configuration function 7 16 7 34 changing the allowed setpoint error 7 23 7 24 changing the pause time out limit 7 22 changing the sample tube time constant 7 30 7 31 MicroAmp reaction tubes 7 30 7 31 Thin walled GeneAmp reaction tubes 7 32 7 34 changing the sample tube type 7 28 7 29 changing the setpoint clock temperature interval 7 26 7 27 description of 7 2 displays in 7 17 entering an idle state setpoint value 7 25 in installation 2 14 2 16 parameters in 7 16 printing configuration parameters 7 34 setting time and date 7 18 7 19 turning runtime beeper on and off 7 20 7 21 turn
179. tal 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 Software Shortcuts Below are some hints to getting around quickly in the software while you are creating or editing programs Using the STOP Key While you are creating or editing a program you may want to start over or use another function of the instrument You can easily do this by using the STOP key 1 With any of the program displays shown press STOP The following display appears Program Type Program Number not yet assigned CYCL j i CYCL xx xC RUN STORE PRINT HOME Returns you to the main menu 2 Press the OPTION key to move the cursor under HOME then press ENTER The following display appears Prog not stored Continue YES 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 the program 5 28 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com
180. tarting a run the following display appears Cover temp is xx C Run starts at 100 C Troubleshooting Information continued Possible Cause The laboratory is either too humid or too hot One of the main instrument systems has failed Suspected poor cycling performance This is normal if you start a run just after turning the instrument on or completing a subambient hold Check and or Remedy Move the instrument to an air conditioned room Or run Diagnostic Test 3 the Chiller Test Call an Applied Biosystems Service Engineer if the test fails Call an Applied Biosystems Service Engineer Run Diagnostic Test 4 System Performance Test then call an Applied Biosystems Service Engineer Wait a few minutes to allow the block cover to come up to temperature If it doesn t contact an Applied Biosystems Service Engineer 9 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Table 9 1 9 4 Problem Upon power up or returning to an instrument that has been running unattended the following display appears Power Fail x min Review history YES The printer is not printing run time data When you turn on the instrument the following display appears Call Service Troubleshooting Information continued Possible Cause This is normal if the power has been interrupted or shut off while running a program The
181. te list of programs 7 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 6 Directory Enter program 1 Press to move forward to Step the next display to move to the previous display to return to the first display to return to the first display to return to the first display Figure 7 2 Example of a list of programs listed according to program number Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Listing Programs by their Program Type TYPE The TYPE selection lets you list all your programs of a specific program type HOLD CYCL or AUTO in numerical order To list your programs by their program type 1 Select DIR on the Utilities menu as described on page 7 3 The Directory display appears Directory PROG TYPE USER PRINT Press OPTION to move the cursor to TYPE then press ENTER The following display appears Directory HOLD CYCL AUTO METH 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 7 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE
182. temperature to another The hold time is the length of the samples will be held at the specified temperature With the GeneAmp PCR System 9600 the hold time begins when the samples not the block reach the target temperature 30 sec Hold Time Ramp Time Time The temperature ramp time and hold time for Setpoint 1 are set up using this display in the CYCL program Setpt 1 Ramp 0 00 94 0C Hold 0 30 Figure 3 2 Setting temperature 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 see that the CYCL program is similar to a form which you can fill out with your thermal cycling instructions Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Starting Up the Instrument Press the power switch see Figure 1 3 to the ON position _ a aaae RA A Power Switch 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 3 5 Artisan Technology Group Quality Instrumentation Guaranteed 888
183. the GeneAmp PCR System 9600 Connect the other end of the cable to the connector on the serial adapter card you just installed Note When you are printing the printer ON LINE OFF LINE button 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 ON 6 OFF 7 OFF 7 OFF 8 OFF 8 OFF 2 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com SW2 and SW1 Viewed from This Side of P C Board DIP switch Settings on the Epson C82302 serial interface card Figure 2 1 2 8 Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Instrumentation RS 232 Communications Pa rameters for users who do G A PCR Syst 9600 not have an LX 810 pcan a eee 9600 Baud No Parity 8 data bits 1 stop bit Instrument Power Cord Connection Printer Dip Switch settings Fuse Holders Serial Port ON OFF 1 sw2 4 Switch ass AN Cable N801 0421 Pa dl O
184. the events that occurred during a run If a run was terminated you can view the History file to determine the cause and how much of the run was completed The History file contains two types of information about a run It includes status records which display general information about the run and 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 History file you can display or print all the status and data records of a run only the status records of a run only those records of a run that contain errors 7 38 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Status Records in a History File As mentioned earlier a status record contains general information about a run Every run has at least four status records that contain the sample tube type the reaction volume the temperature at which the clock started and either a message indicating that the run was completed successfully or a message indicating that an error occurred during the run A status record displays the following information
185. 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Editing a Method When you want to view a stored method or change it so it includes a different sequence of linked programs you use the Edit function To edit a method Access the main menu Select Option 9600 RUN CREATE EDIT UTIL Press the OPTION key to select EDIT then press ENTER You obtain the following display Edit Enter program _ Type the number of the method you wish to edit then press ENTER The following display appears Link progs _ If desired edit the sequence of linked programs 5 23 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 24 Note If you enter a program number for a program that does not exist you will see a message that reads Program not found The next display allows you to choose the program number you want to edit again 5 The last display gives you the option of storing the file Press the OPTION key to select STORE then press ENTER The following display appears Store Enter program x The next available number x appears at the cursor 6 To store the method you have two options You can create a new copy of the
186. 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 7 51 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Running the Chiller Test Diagnostic Test 3 is the Chiller Test which verifies the performance of the refrigeration system by calculating the cooling rate of the sample block CAUTION Before you begin this test make sure you place 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 To run the Chiller Test 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears Enter Diag Test 1 REVIEW HISTORY FILE 2 Select Diagnostic Test 3 by pressing 3 then pressing ENTER or by pressing the STEP key twice The following display appears Enter Diag Test 3 CHILLER TEST 3 Press ENTER to start the test 7 52 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The system first waits for the coolant temperature to get to 10 degrees C If it can t do this within 18 minutes a failure message will be displayed The following display appears Chiller Test
187. the time in hours and minutes HH MM and Date MM DD YY the date in month day and year MM DD YY Press STEP to move to the next display Runtime printer OFF To configure the instrument for use with a printer Runtime beeper ON press the OPTION key to change OFF to ON then press ENTER To turn the run time beeper off press 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 Set the maximum amount of time that a program XX XX 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 Allowed setpt error Set the number of degrees the actual sample X xC temperature may vary before the reading is noted in the History file as an error The default value is 2 0 degrees C Press STEP to move to the next display Or press BACK to move to the previous display 2 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Idle state setpoint Start clock within x xC of setpoint Special tube 2 16 No Set the temperature at which the block will be maintained when a program is not running As factory set the instrument will heat to 25 degrees C while idling and the heating indicator will flash The default idling temperatu
188. thod Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Storing the Method 1 Press the OPTION key to move the cursor beneath STORE then press ENTER The following display appears Store Enter program x X is the next available number If this is the first file being stored x would be a 1 on the display Press ENTER to store the method under the displayed number OR To use a different number type the number 1 150 then press ENTER The following display appears Store Protect program NO 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 5 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 5 22 Store Enter user _ In this display you can specify any number from 1 to 9999 for your user identification number Make a note of the number you choose for later use Type the number then press ENTER The following display appears Prog x User xxxx OK to store YES Note Ifyou 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
189. tion Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Maintenance Introduction This chapter describes how to perform routine maintenance on the GeneAmp PCR System 9600 without the aid of an Applied Biosystems Service Representative WARNING Donot 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Cleaning the Sample Wells The sample wells should be cleaned once a month or as needed WARNING During instrument operation the sample block can be heated as high as 100 degrees C Before performing the following procedure be sure to wait until the sample block reaches room temperature To clean the sample wells 1 Run a 25 degree HOLD program to bring the sample block to room temperature then turn off the instrument for 15 minutes Remove the sample tray from the block and set aside 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 thoroughly with a cotton swab soaked in Chlorox
190. tion Test Use this procedure to verify that your Applied Biosystems GeneAmp PCR System 9600 still meets the temperature accuracy specification Equipment Required You will need the following equipment to perform this procedure Temperature Verification System Part No N801 0435 which includes Digital thermometer with 9V battery installed RTD probe Cotton 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 the forward position turn the cover knob completely counterclockwise then slide the cover back 8 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 2 Using a cotton swab coat wells D1 and E1 with mineral oil Figure 8 1 shows the location of these wells 1 2 3 4 5 6 7 8 9 10 11 12 000000000000 000000000000 000000000000 0000000000 O Front of instrument 0 O gt mMm 160101010101019191010 000000000000 000000000000 H OOOOOOOOOO0OO0O n Figure 8 1 Location of sample wells E1 and D1 3 Place the probe tray on the sample block so that the probe tray notch faces the f
191. tory file beginning with the most recent record STAT view just the status records in the History file ERROR view just the records with error messages PRINT print some or all of the records in the History file 3 Press the OPTION key to move the cursor to your desired selection and press ENTER The last record will be displayed first Note You can skip forward or backward a specified number of records to a specific record by typing the number of records to be skipped followed 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 7 45 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Enter Diag Test 1 REVIEW HISTORY FILE Press History 10 recs ALL STAT ERROR PRINT Press The most recent record Pa is displayed first 10 Press Press Press Status CYCL 2 Record Abort 12 21 90 14 47 Step Back Stop to move to the to move to to return to Ea d c 2 26 00 2 next display the previous the first dis ecor Cyc 3 Setpt 1 0 05 display play CH 2 25 2C 8 CYCL 2 4 Cyc 2 Setpt 2 0 10 Start 12 21 90 14 45 CH 2 29 8C 7 CYCL 2 3 Cyc 2 Setpt 1 0 10 Clk starts w in 1 0C CH 2 25 2C 6 CYCL 2 2 C
192. trument It is caused by the refrigeration motor stalling because it is unable to start until the pressure bleeds away which takes about five minutes S 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Technical Support Contacting Technical Support To Contact Technical Support by E Mail Hours for You can contact Applied Biosystems for technical support by telephone or fax by e mail or through the Internet You can order Applied Biosystems user documents MSDSs certificates of analysis and other related documents 24 hours a day In addition you can download documents in PDF format from the Applied Biosystems Web site please see the section To Obtain Documents on Demand following the telephone information below Contact technical support by e mail for help in the following product areas 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 Spectrometers tsupport appliedbiosystems com LC MS Applied Biosystems MDS Sciex apisupport sciex com or api3 support sciex com Chemiluminescence Tropix
193. u 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 MICRO The default reaction volume is 100 uL Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 4 Ifthe Special Tube parameter in the Configuration function see Chapter 7 has been set to NO pressing the OPTION key will change the tube type to Thin Walled GeneAmp Reaction Tubes On the display MICRO changes to THIN Note Instructions for the use of sample tubes other than MicroAmp Reaction Tubes will be included in separate documentation 5 If the Special Tube parameter in the Configuration function see Chapter 7 has been set to YES pressing the OPTION key twice 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 reaction volume you selected will be used as defaults For methods the tube type and reaction volume you select before you run the method will be used for every program in that method 6 13 Artisan Te
194. u want an increase or decrease in the hold time then press ENTER 4 Enter the time by which 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 Setpt 2 55 0C temperature PCR the default temperature is 55 Change time temp NO degrees C For a two temperature PCR the default is 68 degrees C Setpt 2 55 0C Hold for 0 30 To change these displays use the same procedure as described for Setpoint 1 5 42 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Setpt 3 72 0C Hold for 0 30 Setpt 3 72 0C Change time temp NO Setpt n 0 0C Hold for 0 30 Total cycles 25 Pause during run NO These two displays are used to set the temperature and hold time for the third setpoint Setpt 3 and change the time and temperature values in successive cycles if desired To change these displays use the same procedure as described for Setpoint 1 A display will appear for each setpoint up until the total number of setpoints specified in the first program display For each setpoint you will be asked whether you want to change the time or temp
195. uaranteed 888 88 SOURCE www artisantg com Specifications Dimensions The physical dimensions of the instrument are Height 30 5 cm 12 in Width 52 cm 20 in Depth 61 cm 24 in Weight 40 5 kg 90 Ibs Sample Compartment 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Power Requirements Control Panel Display Keypad Indicator Lights 10 2 There are three versions of the GeneAmp PCR System 9600 The power requirements of these instrument versions are 120VAC 60 Hz 10 amps 15 amp slow blow fuse 220 240 VAC 50 Hz 5 amps 8 amp slow blow fuse 100 VAC 50 60 Hz 12 amps 15 amp slow blow fuse The instrument control panel consists of the display keypad and indicator lights 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 The keypad consists of nine function keys and ten numeric keys There are three indicator lights Heating Cooling Hot Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www
196. ves under UTIL Select Option 9600 RUN CREATE EDIT UTIL 3 Press ENTER The utilities menu is displayed Select function DIR CONFIG DIAG DEL 4 Press the OPTION key once to move the cursor under CONFIG then press ENTER to select configuration 2 12 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The following display appears Time HH MM Date MM DD YY This display is used to set the time and date 5 To set the time press the appropriate numeric keys for hours and minutes HH MM then press ENTER The software will place the colon for you Press ENTER after making each entry 6 To set the date press the appropriate numeric keys for month day and year MM DD YY then press ENTER The software will separate the numbers for you 7 Press STEP The following display appears Runtime printer OFF Runtime beeper ON This display lets you turn the run time printer mode and the run time beeper 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 key to toggle the ON on the bottom line of the display to OFF then press
197. w the MORE key works O Ramp to 96 5C xx xC 0 30 Cycle 1 Press To move between Setpt 1 Tot Cyc 30 the two run time dis Hrs left 0 7 Prog 1 plays 8 After a few moments press the STOP key to abort the run The following display appears CYCL 1 xx xC Abort program YES 9 Press the ENTER key to stop the program A display similar to the one shown below appears 3 26 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Next Step CYCL 1 Abort xx xC RUN STORE PRINT HOME 10 You can now return to the main menu Press the OPTION key to move the cursor to HOME then press ENTER Select Option 9600 RUN CREATE EDIT UTIL In this tutorial you have learned how to set up a three temperature PCR CYCL program You may now want to try creating a CYCL program to perform two temperature PCR Start by selecting CREATE on the main menu Then select CYCL for the type of program you want to create Enter 2 in the first display 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 information on loading and running your
198. wo 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 program The original program 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com b Type the original number for the program then press ENTER This allows you to replace the original program with the new edited version The subsequent display will ask OK to overwrite Select YES and the original program will be over written by the new edited version If the original 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 Prog x is protected Enter user 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 5 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOU
199. y which holds 480 tubes See Chapter 5 for details Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Comparing Files and Programs In the GeneAmp PCR System 9600 software PCR files are referred to as programs The following table lists the differences between DNA Thermal Cycler PCR files and GeneAmp PCR System 9600 PCR programs Function PCR INCUBATIONS PCR CYCLING AUTO SEGMENT EXTENSION METHODS File on the DNA Thermal Cycler SOAK File 1 An incubation file TIME DELAY File 2 An incubation file THERMO CYCLE File 3 Use the 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 THERMO CYCLE or STEP CYCLE with auto segment extension Link each file to another file using the link to stored file parameter within each file Program on the GeneAmp PCR System 9600 HOLD Set the hold time to the FOREVER option for an indefinite soak HOLD Set the hold time to a pre defined time 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 This program can automatically increase or decrease the setpoint hold time and setpoint temperature in successive cycles METH Use this program to link together a series of program
200. yc 1 Setpt 2 0 10 Reaction vol 100uL CH 2 29 9C 5 CYCL 2 1 Cyc 1 Setpt 1 0 10 Tube type MICRO Figure 7 11 Viewing ALL the records in a History file for a two temperature CYCL program Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Enter Diag Test 1 REVIEW HISTORY FILE History 10 recs ALL STAT ERROR PRINT Press to return to the first display CYCL 2 10 Abort 12 21 90 14 47 If no error occurs during a run No Error records will appear on the display If an error occurs dur ing a run a data record contain ing an error message will appear here Status Message History Print ALL STAT ERRORS Select this option to print only those data recorc with error messages Select this option to print all status and data records Select this option to print only status records Figure 7 12 Viewing the status STAT records data records with error messages ERROR and printing records PRINT Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 7 48 Printing the History file To print the History file 1 Select DIAG on the Utilities menu as described on page 7 3 The following display appears Enter Diag Test 1 REVIEW HISTORY FILE 2 Press ENTER to select Diagnostic Test 1 The following display appears History 10 recs ALL STAT ERROR PRINT

GeneAmp® PCR System 9600 - Artisan Technology Group

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GeneAmp® PCR System 9600 - Artisan Technology Group