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Page 2 GeneAmp ® PCR System 9600 User’s Manual Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 3 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 Chain Reaction (PCR) process, which are owned by Roche Molecular Systems, Inc.
Page 4 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.
Page 5 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 instrument) that could cause personal injury or instrument damage if precautions are not followed. This can be any type of hazard.
Page 6 Additional graphic symbols used on the instrument are the following: Indicates alternating current. Indicates the primary protective grounding terminal. Indicates the off position of the main power switch. Indicates the on position of the main power switch. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 7 électriques, ne pas ouvrir les couvercies si un outil est nécessaire. Ne contient aucune pièce pouvant être réparée par l'utilisateur. Confier le dépannage au personnel qualifié de Applied Biosystems. Left Side of Instrument ! WARNING ! For protection against fire hazard, replace only with same type and rating of fuse.
Page 8 Pour éviter les chocs électriques, débrancher le cordon d'alimentation avant le dépannage. CAUTIONThis unit contains protective circuitry. Contact Applied Biosystems Service before performing any AC line tests. ! AVERTISSEMENT ! Cet appareil contient des circuits de protection. Vérifier auprès de Applied Biosystems avant d' effectuer des essais de secteur.
Page 9 électriques, ne pas ouvrir les couvercies si un outil est nécessaire. Ne contient aucune pièce pouvant être réparée par l'utilisateur. Confier le dépannage au personnel qualifié de Applied Biosystems. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 10 ! 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 même type et de même courant nominal.
Page 11 Pour éviter les chocs électriques, débrancher le cordon d'alimentation avant le dépannage. CAUTIONThis unit contains protective circuitry. Contact Applied Biosystems service before performing any AC line tests. ! AVERTISSEMENT ! Cet appareil contient des circuits de protection. Vérifier auprès de Applied Biosystems avant d' effectuer des essais de secteur.
Page 12 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 reconnect the surge components.
Page 13 Operating Precautions 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.
Page 14 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.
Page 15 Pollution Degree This equipment will operate safely in environments that contain nonconductive foreign matter up to Pollution Degree 2 in IEC 1010–1, CSA 1010.1 and UL 3101–1. Storage Conditions 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.
Page 16 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 instrument.
Page 17 Technical Support Contacting You can contact Applied Biosystems for technical support by telephone or fax, by e-mail, or through the Internet. You can order Applied Technical Support 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”...
Page 18 In North America To Contact Technical Support To contact Applied Biosystems Technical Support, use the telephone or by 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.)
Page 19  and Cytofluor 4000 then press Fluorescence Plate Reader Chemiluminescence 1-781-275-8581 1-800-542-2369 (Tropix) (U.S. only), 1-781-271-0045 Applied Biosystems/MDS 1-800-952-4716 1-650-638-6223 Sciex Outside North America Telephone Region Dial... Dial... Africa and the Middle East Africa (English Speaking) 27 11 478 0411...
Page 20 Telephone 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 2 593 6470/6471 82 2 593 6472 Malaysia (Petaling Jaya) 60 3 758 8268...
Page 21 You can also order technical documents or an index of Through the available documents and have them faxed or e-mailed to you through Internet 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 Access the Applied Biosystems Technical Support Web site.
Page 22 Free, 24-hour access to Applied Biosystems technical documents, To Obtain including MSDSs, is available by fax or e-mail or by download from our Documents on Web site. Demand To order documents... Then... by index a. Access the Applied Biosystems Technical Support...
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Page 24: Chapter 6. Running Pcr Samples
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.
Page 25 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 instrument power loss.
Page 26 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.
Page 27 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.
Page 28 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 File on the DNA...
Page 29 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,...
Page 30 File Storage 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 user files. Operation On the DNA Thermal Cycler, the run-time display counts down the number of cycles.
Page 31 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...
Page 32 Graphic 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...
Page 33 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).
Page 34 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.
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Page 36: Table Of Contents
Chapter 2. Installing the GeneAmp PCR System 9600 ....2-1 Introduction ......... . . 2-1 Unpacking .
Page 37 Configuring the Printer ....... 2-12 Configuring the GeneAmp PCR System 9600 ....2-14 Summary of Configuration Parameters .
Page 38 Chapter 4. Software Basics ........4-1 Introduction .
Page 39 Software Shortcuts ........5-28 Using the STOP Key ....... . 5-28 Recalling Programs: A Shortcut .
Page 40 Indicator Lights ........6-16 Run-Time Displays .
Page 41 THIN Time Constant ......7-32 Printing the Configuration Parameters ....7-34 The Diagnostic Function (DIAG) .
Page 42 Testing the Temperature Uniformity ....8-13 Test Results ........8-17 Changing External Fuses .
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Page 44 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 ......5-3...
Page 45 Sample conversion of hold times for down ramps (DNA Thermal Cycler to GeneAmp PCR System 9600) ..... 5-7 Figure 5-4 Editing Keys .
Page 46 ........8-9 Figure 8-4 GeneAmp PCR System 9600 Calibration Label....8-10 Figure 8-5 The probe assembly in sample wells A1 and A2.
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Page 48: Preface: Using The Manual
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...
Page 49 We recommend that you follow this approach to learn about the GeneAmp PCR System 9600: 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.
Page 50: Conventions
Conventions The following conventions are used in this manual. Software Conventions The instrument display is pictured as follows. 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.
Page 51: Notes And Warnings
Notes and Warnings 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.
Page 52: Chapter 1. Introducing The Geneamp ® Pcr System 9600
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 - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 53: Principles Of Operation
Principles of Operation 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.
Page 54: Instrument Description
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.
Page 55: A Look At The Control Panel
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 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;...
Page 56: Instrument Features
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...
Page 57 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...
Page 58: Chapter 2. Installing The Geneamp Pcr System 9600
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: Parts Supplied Power Requirements Proper Location...
Page 59: Unpacking
Unpacking 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.
Page 60: Supplies, Accessories, And Replacement Parts
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.
Page 61: Power Requirements
(15 degrees C to 30 degrees C). The GeneAmp PCR System 9600 operates on one of the following input voltages: Maximum Operating Voltage Freq.
Page 62: Proper Location
7/7). If you need a power 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.
Page 63: Setting Up The Printer
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).
Page 64 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 the GeneAmp PCR System 9600. Connect the other end of the cable to the connector on the serial adapter card you just installed.
Page 65 Figure 2-1 DIP switch Settings on the Epson C82302 serial interface card. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 66 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. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 67: Installing The 230-Vac Printer
Installing the 230-VAC Printer 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).
Page 68 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. 2-11...
Page 69: Configuring The Printer
Configuring the Printer 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"...
Page 70 The following display appears: Time HH:MM Date MM/DD/YY This display is used to set the time and date. 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.
Page 71: Configuring The Geneamp Pcr System 9600
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...
Page 72: Summary Of Configuration Parameters
Summary of Configuration Parameters This display lets you edit or print the configuration Configuration parameters. EDIT-PRINT Press ENTER to select EDIT. The first configuration screen, used to set the time and date, is displayed. Set the time in hours and minutes (HH:MM), and Time HH:MM the date in month, day, and year (MM/DD/YY).
Page 73 Set the temperature at which the block will be Idle state setpoint 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 temperature may be changed to a new value.
Page 74 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.
Page 75 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. 2-18 Artisan Technology Group - Quality Instrumentation ...
Page 76: Heater And Chiller Tests
Heater and Chiller Tests After you have configured the GeneAmp PCR System 9600, perform the heater and chiller tests as described in the following sections to verify that the instrument is operating correctly. Heater Test The heater test verifies that the sample block heaters and electronics are operating correctly.
Page 77 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 Press STOP to go to the next test (Test #3).
Page 78: 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. Chiller Test Passed Press STOP to exit the test. The next test (Test #4) will appear on the display.
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Page 80: Tutorial: Customizing A Pcr Cycl Program
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...
Page 81: Before You Start
Before You Start Before you start this tutorial: The system should be properly installed either by an Applied Biosystems service representative or according to the supplied instructions in Chapter 2, Installation, in this manual. Read Chapter 1 in this manual. Unwrap one of the MicroAmp Trays supplied with the instrument.
Page 82: What Is A Cycl Program
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.
Page 83 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.
Page 84: Starting Up The Instrument
Starting Up the Instrument Press the power switch (see Figure 1-3) to the ON position. Figure 3-3 Location of power switch. A beeper sounds, and all three indicator lights on the control panel flash. The screen lights up and a series of displays appear. Artisan Technology Group - Quality Instrumentation ...
Page 85: Getting To The Cycl Program
Getting to the CYCL Program 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.
Page 86 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: b. When the cursor reaches the last selection (UTIL), press OPTION to move the cursor to the first selection again: The OPTION key is used the same way on many different displays.
Page 87 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 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.
Page 88: A Look At The Cycl Program
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.
Page 89 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.
Page 90 The following display appears: Total cycles = 25 Pause during run? NO 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 Press the previous...
Page 91 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.
Page 92 Figure 3-4 Moving through the CYCL program displays. 3-13 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 93: Customizing The Cycl Program
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 The first display in the CYCL program (shown below) should appear on your display.
Page 94: Defining Values For Setpoint # 1
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. Look for the cursor on the display. It appears under the ramp time. The default time of 0:00 is most commonly used.
Page 95 The cursor moves to the hold time: Setpt #1 Ramp 0:00 96.0C Hold 0:30 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...
Page 96: Defining Values For Setpoint #2
Defining Values for Setpoint #2 Setpt #2 Ramp 0:00 55.0C Hold 0:30 Use the default ramp time by pressing ENTER Enter 52.5 degrees C for the temperature by pressing 5, then 2, then 5. Then press ENTER. We will not change the hold time, Press STEP to skip over this entry, The display for Setpoint #3 appears.
Page 97: Specifying The Number Of Cycles
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. Enter 30 cycles: press 3 then press 0. When the entry is correct, press ENTER.
Page 98 The next display (the last display in the program) is: Program Type Program Number not yet assigned CYCL CYCL#??? 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 that the program doesn’t have a program number yet since it hasn’t been stored.
Page 99: Storing Your Cycl Program
Storing Your CYCL Program The following display should appear on your screen: CYCL#??? xx.xC RUN-STORE-PRINT-HOME Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # 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”...
Page 100 The following display appears: Prog# OK to store? YES Press ENTER to store the program The following display appears: Program Type Assigned Program Number (1) CYCL CYCL# xx.xC RUN-STORE-PRINT-HOME On 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.
Page 101: Starting A Trial Run
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.
Page 102 Figure 3-5 Sliding the heated cover forward for a trial run. 3-23 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 103: Running The Program
Running the Program 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 With the cursor beneath RUN, press ENTER. The following display appears: Enter program # _ Press the key for the number of the program you created and stored earlier in this tutorial.
Page 104 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 temperature...
Page 105 Current setpoint number Total cycles in program Setpt #1 Tot Cyc 30 Hrs left 0.7 Prog Estimated time left in Current program # program Press MORE again to return you to the first run-time display. The illustration below shows you how the MORE key works. Ramp to 96.5C xx.xC 0:30...
Page 106: 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 The Next Step In this tutorial, you have learned how to set up a three- temperature PCR CYCL program.
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Page 108: Software Basics
Software Basics Introduction ® This chapter presents an overview of the GeneAmp 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...
Page 109: Reviewing Keypad Basics
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.
Page 110: Use Of The Keys
Use of the Keys 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.
Page 111: A Close Look At The Main Menu
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. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 112: Selecting A Function
Selecting a Function 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. 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.
Page 113: An Overview Of Pcr Programs And Methods
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.
Page 114: Storing Programs And Methods
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.
Page 115: The Hold Program
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 running a CYCL program.
Page 116 Figure 4-4 A HOLD program held for an indefinite time. Figure 4-5 A HOLD program held for a specific time interval. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 117: Cycl: The Cycle Program
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.
Page 118 Figure 4-6 A common CYCL program 4-11 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 119: The Auto Program
The AUTO Program 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.
Page 120 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...
Page 121: Pcr Methods
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).
Page 122: Setting Up Pcr Programs And Methods
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.
Page 123: Setting Hold Times On The Geneamp ® Pcr System 9600
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...
Page 124 Figure 5-1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 125 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).
Page 126: Sample Conversion Of Hold Times For Up Ramps (Dna Thermal Cycler To Geneamp Pcr System 9600)
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.
Page 127 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.
Page 128 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 Table 5-2 be used on the DNA Thermal Cycler, you can also use convert the hold times.
Page 129: Editing Keys
Editing Keys To create, view, or edit programs and methods, you will use the following keys. 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.
Page 130: Creating And Editing Programs
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. Start at the main menu. Choose one of the following: a. Select CREATE on the main menu if you want to create a new program.
Page 131: Creating A Program
Creating a Program Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL Press the OPTION key to select CREATE, then press ENTER. The following display appears Create a program HOLD-CYCL-AUTO-METH Press the OPTION key to select the type of program — HOLD, CYCL, or AUTO —...
Page 132: Storing The Program
Storing the Program Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # 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.
Page 133 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...
Page 134: Editing A Program
Editing a Program When you want to view a program you have stored or make changes to it, you 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.
Page 135 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. Edit the program as necessary. The displays in each program are described in the tables at the end of this chapter.
Page 136 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.
Page 137: Printing A Program
STOP.) CYCL#??? xx.xC RUN-STORE-PRINT-HOME Press the OPTION key twice to select PRINT, then press ENTER. The program is printed. GeneAmp PCR System 9600 Ver 2 June 1, 1992 10:52 am CYCL Progr- #??? — Program Parameters 3 Temperature PCR...
Page 138: Creating And Editing Methods
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. Start at the main menu. Choose one of the following: a. On the main menu, select CREATE if you want to create a new method.
Page 139: Creating A Method
Creating a Method 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...
Page 140 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.
Page 141 The last display to appear when you are creating a method allows you to run, store, or print the method: Program Type: Program Number (not yet assigned) (Method) METH#??? xx.xC RUN-STORE-PRINT-HOME In most cases, you will want to store the method and assign it a number so that it can be run at any time.
Page 142: Storing The Method
Storing the Method Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # 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.
Page 143 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...
Page 144: Editing A Method
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.
Page 145 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. The last display gives you the option of storing the file. Press the OPTION key to select STORE, then press ENTER.
Page 146: Printing A Method
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.
Page 147 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. GeneAmp PCR System 9600 Ver 2 June 1, 1992 10:55 am...
Page 148: Example Of A Method Printout Using Program Data
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 #l...
Page 149: Software Shortcuts
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.
Page 150 A shortcut to the above procedure is: With any of the program displays shown, press STOP. The following display appears: CYCL#??? xx.xC RUN-STORE-PRINT-HOME 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.
Page 151: Recalling Programs: A Shortcut
Recalling Programs: A Shortcut Once you have finished editing or running a program, you can quickly recall another program without needing to return to the main menu. Once you have stored a program, your display will look like this (CYCL program shown): Program Type: Program Number (26) CYCL# 26...
Page 152: The Hold Program
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.
Page 153: Description Of Hold Program Displays
Description of HOLD Program Displays This display allows you to set the temperature at Hold at 4.0C which the sample will be held and the length of time Hold FOREVER- 10:00 this temperature will be maintained. Press ENTER to accept the default temperature (4 degrees C), or select a different temperature.
Page 154: Cycl: The Cycle Program
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.
Page 155: Description Of Cycl Program Displays
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. 5-34 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 156 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: For the 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.
Page 157 Setpoint #3 in a typical cycle program is used for Setpt #3 Ramp 0:00 primer extension. This display sets the ramp time, 72.0C Hold 0:30 target temperature, and hold time for the third setpoint (Setpt #3). The default values are shown in the display to the left.
Page 158 The display appears only if you specified a pause in Pause after setpt #1 the previous display. ln this display, you define the Beep while pause?YES setpoint after which you want to pause the run. Type the number of the desired setpoint, then press ENTER.
Page 159 The last display in the program indicates the CYCL #??? xx.xC program type, followed by “???,” which means that RUN-STORE-PRINT-HOME 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.
Page 160: The Auto Program
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 Figure 5-10 The main displays in a three-temperature AUTO program. 5-39 Artisan Technology Group - Quality Instrumentation ...
Page 161: Description Of Auto Program Displays
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.
Page 162 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. Specify the hold time in minutes and seconds, then press ENTER.
Page 163 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. Press ENTER to accept the default (0.0) temperature. This will not change the specified temperature of Setpoint #1 in successive cycles.
Page 164 These two displays are used to set the temperature Setpt #3 72.0C and hold time for the third setpoint (Setpt #3) and Hold for 0:30 change the time and temperature values in successive cycles, if desired. Setpt #3 72.0C To change these displays, use the same procedure Change time/temp? NO as described for Setpoint #1.
Page 165 The display appears only if you specified a pause in Pause after setpt #1 the previous display. In this display, you define the Beep while pause?YES setpoint after which you want to pause the run. Type the number of the desired setpoint, then press ENTER.
Page 166 The last display in the program indicates the AUTO# ??? xx.xC program type, followed by “???,” which means that RUN-STORE-PRINT-HOME 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.
Page 167 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 168: Running Pcr Samples
Running PCR Samples6 Introduction To run samples, turn on the instrument and follow these procedures, which are explained in this chapter. 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...
Page 169: Loading Samples
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).
Page 170: Setting Up The 96-Position Sample Tray
Figure 6-1 Setting up the 96-position sample tray. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 171: Securing The Retainer On The Tray
Note When using MicroAmp Reaction Tubes with Caps, place the required number of tubes into 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.
Page 172: Placing The Sample Tray In The Block
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.
Page 173: Sliding The Heated Cover Forward
Make certain that the cover knob is completely counterclockwise, which fully raises the platen, before you attempt to slide the heated cover forward. Then slide the cover forward. Figure 6-4 Sliding the heated cover forward. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 174: Turning The Cover Knob
Turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover (indicating the full clockwise position). This lowers the platen onto the tray. Figure 6-5 Turning the cover knob. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 175: Using The Cap-Installing Tool
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. Place individual sample tubes or a row of tubes in the sample tray (you don't have to use a retainer).
Page 176: Removing Samples From The Tray
Removing Samples from the Tray The following procedure describes how to remove the sample tubes from the tray: 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).
Page 177: Specifying A Program Or Method
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.
Page 178: Starting The Run
Starting the Run Run Keys The following keys are used to start a run or are used during the run. Figure 6-7 Run-Time Keys The function of each key is described below. Starts or restarts a sample run. MORE Displays more information about run-time parameters.
Page 179: Running A Stored Program
Running a Stored Program To run a program that you have previously stored: 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.
Page 180 If the “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.
Page 181 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”...
Page 182: An Example Printout Of A Cycl Program Using The Setpoint Option
Figure 6-8 An example printout of a CYCL program using the SETPOINT option. ! WARNING ! During a sample run, keep the heated cover pulled forward and tightened down at all times. This will guard against burns and guarantee the best temperature uniformity. 6-15 Artisan Technology Group - Quality Instrumentation ...
Page 183: Indicator Lights
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.
Page 184: Run-Time Displays
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.
Page 185 Ramp to 94.0C xx.xC 0:30 Cycle 1 Press More To move between the Setpt #1 Tot Cyc 30 two run-time displays Hrs left 0.5 Prog Figure 6-10 Using the MORE key. The parameters in the second run-time display are explained in Figure 6-11.
Page 186: Hold Program Run-Time Display
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. Programmed target Current sample temperature temperature Hold at 95.0C...
Page 187: Pausing A Run
Pausing a Run 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 if 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.
Page 188 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. If you change your mind and do not want to abort the run, press the OPTION key to change “YES”...
Page 189: Reviewing The History Of The Run
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 the 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.
Page 190: Utilities
Utilities Introduction This chapter explains the Utilities functions. The Utilities functions let you: display or print programs by their 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)
Page 191: Getting To The Utilities Menu
Getting to the Utilities Menu To get the Utilities menu: Get to the Main menu. Press the STOP key once or twice until the Main menu appears: Select Option 9600 RUN-CREATE-EDIT-UTIL Press the OPTION key three times to move the cursor to UTIL, then press ENTER.
Page 192: Selecting A Utilities Function
Selecting a Utilities Function To select one of the Utilities functions: 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. When the cursor is under your desired selection, press ENTER. You will then see the first display for the function you selected.
Page 193: The Directory Function (Dir)
The Directory Function (DIR) The Directory function lets you display or print programs according to: program 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...
Page 194 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.
Page 195 Directory Enter program # Press to move forward to Step the next display Press HOLD #1 Stop to return to the first display Press to move to the previous Step Back display Press CYCL #2 Stop to return to the first display Step Back...
Page 196: Listing Programs By Their Program Type (Type)
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: Select DIR on the Utilities menu as described on page 7-3. The Directory display appears: Directory PROG-TYPE-USER-PRINT...
Page 197 For example, if your first HOLD program is HOLD #14, the following display appears: HOLD #14 Press STEP to view the next display in your program listing. In our example, the next HOLD program is HOLD #26: HOLD #26 Press BACK each time you want to view the previous program in the list.
Page 198: Example Of A List Of Programs Listed According To Program Type
Directory HOLD-CYCL-AUTO-METH Press to move forward to the next display Step Press HOLD #14 Stop to return to the first display to move to the Press previous display Step Back Press HOLD #26 Stop to return to the first display Back Step Press...
Page 199: Listing Programs By Their User Number (User)
Listing Programs by their User Number (USER) 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.
Page 200 Press STEP to view the next display. In our example, CYCL program #6 is listed: CYCL #6 User#7777 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...
Page 201: Example Of A List Of Programs Listed According To User Number
Directory Enter user #7777 Press to move forward to the next display Step Press HOLD #16 User#7777 Stop to return to the first display to move to the Press previous display Step Back Press User#7777 HOLD #25 Stop to return to the first display Step Back...
Page 202: Printing A Directory Of Your Programs (Print)
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: Select DIR on the Utilities menu as described on page 7-3. The Directory display appears: Directory PROG-TYPE-USER-PRINT...
Page 203 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.
Page 204 Figure 7-5 shows all the displays in the PRINT selection of the Directory function. Figure 7-5 The PRINT selection of the Directory function. 7-15 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 205: The Configuration Function (Config)
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 (on or off) pause time-out limit allowed setpoint error idle state setpoint temperature interval that triggers the clock start sample tube time constants...
Page 206 Configuration EDIT-PRINT Press to display the first Enter configuration parameter Time HH:MM Date MM/DD/YY Runtime printer Step Runtime beeper moves you Pause time-out limit forward to the next display xx:xx Allowed setpt error Back x.xC moves you to the previous dis- Idle state setpoint play or parameter...
Page 207: Setting The Time And Date
Setting the Time and Date 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: Select CONFIG on the Utilities menu as described on page 7-3. The following display appears: Configuration EDIT-PRINT...
Page 208 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. 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 ...
Page 209: Turning The Run-Time Printer Mode And Run-Time Beeper On Or Off
Turning the Run-Time Printer Mode and Run-Time Beeper On or Off The Configuration function lets you turn the run-time printer mode on or 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.
Page 210 The default condition of the run-time beeper is on. To turn the beeper off, press OPTION (ON changes to OFF), then press ENTER. 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.
Page 211: Changing The Pause Time-Out Limit
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 restart a run within 10 minutes after you pause it, the run is aborted.
Page 212: Changing The Allowed Setpoint Error
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.
Page 213 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. 7-24 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 214: Entering An Idle State Setpoint Value
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.
Page 215: Changing The Temperature Interval For The Setpoint Clock
Changing the Temperature Interval for the Setpoint Clock 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.
Page 216 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. To enter a temperature interval different from the default value, press the appropriate numeric keys, then press ENTER.
Page 217: Changing The Sample Tube Type
Changing the Sample Tube Type The Configuration function lets you specify a future sample tube type by defining the tube time constant characteristics. 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: Select CONFIG on the Utilities menu as described on page 7-3.
Page 218 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). Press ENTER. The following display appears: Rxn vol=100uL T= 9.5 Rxn vol= 50uL T= 7.0...
Page 219: Setting Sample Tube Time Constants
Setting Sample Tube Time Constants 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.
Page 220 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 µ display: one for sample tubes with a reaction volume of 100 L, and µ...
Page 221: Thin Time Constant
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 follows: Select CONFIG on the Utilities menu as described on page 7-3. The following display appears: Configuration EDIT-PRINT...
Page 222 These displays let you change the sample tube time constant. There are two default values for sample tube time constants on this µ display: one for sample tubes with a reaction volume of 100 L, and µ one for sample tubes with a reaction volume of 50 L.
Page 223: Printing The Configuration Parameters
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-µL reaction volume. When initiating a PCR program, specify a reaction volume of 20 µL for all experiments using Thin-Walled GeneAmp Reaction Tubes.
Page 224: The Diagnostic Function (Diag)
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...
Page 225: Selecting The Diagnostic Tests
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 You can use the STEP key to scroll forward through the test displays and the BACK key to scroll backward through the test displays.
Page 226 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 REVIEW HISTORY FILE...
Page 227: Reviewing The History File
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 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.
Page 228: Status Records In A History File
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.
Page 229 Any one of the following messages can appear on a status record display: “Tube Type xxxx” This message shows the sample tube type, and will always be the first record. “Reaction Vol xxxxuL” This message shows the reaction volume used in the run, and will always be the second record.
Page 230: A Typical Status Record Display
“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.
Page 231: Data Records In A History File
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, has only one data record. Data records include the following information: record number ending setpoint temperature cycle number (except in HOLD programs)
Page 232 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°...
Page 233: Displaying The History File
Ending Setpoint Program Temperature Type Program # Record # C# 2 25.2C Cyc 1 Setpt 2 0:10 Elapsed Time Cycle # Setpoint # 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.
Page 234 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: view all the records in the History file beginning with the most recent record STAT view just the status records in the History file...
Page 235 Enter Diag Test #1 REVIEW HISTORY FILE Press Enter History 10 recs ALL-STAT-ERROR-PRINT Press Enter The most recent record is displayed first. Press Press Press CYCL# 2 Status Record Abort 12/21/90 14:47 Step Back Stop to move to to move to the to return to C# 2 26.0C...
Page 236: Messages (Error), And Printing Records (Print)
Enter Diag Test #1 REVIEW HISTORY FILE History 10 recs Enter ALL-STAT-ERROR-PRINT Press Stop to return to the first display Enter Enter Enter CYCL# 2 If no error occurs during a run, “No Error records” will appear on Abort 12/21/90 14:47 the display.
Page 237: Printing The History File
Printing the History file To print the History file: Select DIAG on the Utilities menu as described on page 7-3. The following display appears: Enter Diag Test #1 REVIEW HISTORY FILE Press ENTER to select Diagnostic Test #1. The following display appears: History 10 recs ALL-STAT-ERROR-PRINT...
Page 238 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. Figure 7-13 Printout of all status and data records (ALL) of a typical History file.
Page 239: Running The Heater Test
Running the Heater Test 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.
Page 240 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. Press STOP to return to the first Diagnostic display.
Page 241: Running The Chiller Test
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.
Page 242 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. Press STOP to return to the first Diagnostic display.
Page 243: Running The System Performance Test
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.
Page 244 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. Review the test results with an Applied Biosystems Service Engineer. The Service Engineer will use the results to identify the instrument problem.
Page 245: Running The Verify Calibration Test
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.
Page 246: The Delete Function (Del)
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.
Page 247 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. 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.
Page 248: Deleting Programs By User Number
Deleting Programs by User Number To delete all of the programs stored under a specified user number 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.
Page 249 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.
Page 250: Deleting All Unprotected Programs
Deleting All Unprotected Programs You can delete any program, provided that it is not linked in a method or protected under a user number. To delete all unprotected programs: Select DEL on the Utilities menu as described on page 7-3. The following display appears: Delete PROGRAM-USER-ALL...
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Page 252: Maintenance
PCR System 9600 without the aid of an Applied Biosystems Service Representative. Do not remove the instrument cover. There ! WARNING ! 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.
Page 253: Cleaning The Sample Wells
Cleaning the Sample Wells The sample wells should be cleaned once a month or as needed. During instrument operation, the sample ! WARNING ! 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.
Page 254: Cleaning The Heated Cover
Cleaning the Heated Cover The heated cover should be cleaned once a month or as needed. During instrument operation, the heated ! WARNING ! 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.
Page 255: Temperature Calibration Verification Test
Temperature Calibration Verification 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)
Page 256: Location Of Sample Wells E1 And D1
Using a cotton swab, coat wells D1 and E1 with mineral oil. Figure 8-1 shows the location of these wells. Figure 8-1 Location of sample wells E1 and D1. Place the probe tray on the sample block so that the probe tray notch faces the front of the instrument.
Page 257 Turn on the digital thermometer by moving the ON-OFF/RANGE switch to the 200 position. Turn on the GeneAmp PCR System 9600. The main menu appears: Select Option 9600 RUN-CREATE-EDIT-UTIL Press the OPTION key three times to move the cursor to UTIL, then press ENTER.
Page 258 Select function DIR-CONFIG-DIAG-DEL Press the OPTION key twice to 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.
Page 259 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...
Page 260: Temperature Measurements In The Temperature Calibration
When the clock reaches three minutes, the following display appears: Record Temperature Time=MM:SS Blk=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.
Page 261: Test Results
Figure 8-4 GeneAmp PCR System 9600 Calibration Label. Note If you have more than one GeneAmp PCR System 9600 in your laboratory, make sure that the serial number on the calibration label matches the serial number on the instrument you are testing.
Page 262 40-degree C hold: Block Average at 40 °C = T(40) – Low Offset If the block average is more than 0.75 degree C above or below 40 degrees C, your GeneAmp PCR System 9600 needs to be recalibrated. For example: If the measured temperature of well E1 was 39.9°C, and the Low...
Page 263 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. 8-12 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 264: Temperature Uniformity Test
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: If the heated cover is in the forward position, turn the cover knob completely counterclockwise, then slide the cover back.
Page 265 Turn on the digital thermometer by moving the ON-OFF/RANGE switch to the 200 position. Turn on the GeneAmp PCR System 9600 and set up a two-temperature CYCL program with the following parameters: Setpoint #1 Temperature = 95°C...
Page 266 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. 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.
Page 267: Location Of Wells Used In Uniformity Test
10 After you measure the second temperature of well A1, turn the cover knob completely counterclockwise, then slide the heated cover back. 11 Move the probe assembly to wells A4 and A5 with the dummy probe in A5. 12 Slide the heated cover forward and turn the cover knob clockwise until the white marks are aligned.
Page 268: Test Results
If either result is greater than 1°C, your GeneAmp PCR System 9600 must be serviced by an Applied Biosystems Service Representative. 8-17 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
Page 269: Changing External Fuses
Use 8-Amp slow-blow fuses for the 220-240 VAC instruments. See Chapter 10 for information on power requirements. Turn off the GeneAmp PCR System 9600 and disconnect the power cord from the instrument. The fuses are located next to the instrument power cord connection (see Figure 8-8).
Page 270: Chapter 9. Troubleshooting
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,...
Page 271 Diagnostic Test #5 and the Temperature Verification System (Applied Biosystems Part No. N801-0435). The heating or cooling There is a possible Run Diagnostic Test #2 is too slow. controller or mechanical (Heater Test) and #3 malfunction.
Page 272 Or temperatures. run Diagnostic Test #3, the Chiller Test. Call an Applied Biosystems Service Engineer if the test fails. An error message is One of the main Call an Applied...
Page 273 Table 9-1 Troubleshooting Information (continued) Problem Possible Cause Check and / or Remedy Upon power-up or This is normal if the power Review the history file to returning to an has been interrupted or determine when the instrument that has shut off while running a power failed.
Page 274: If The Instrument Turns Off
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.
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Page 276: Chapter 10. Specifications
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 lbs.) Sample Compartment The sample compartment contains an aluminum block with 96 sample positions in an eight by twelve microplate format.
Page 277: Power Requirements
Power Requirements 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...
Page 278: Sample Temperature Range
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.
Page 279: Ramp Time Repeatability
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 ...
Page 280: Printer Interface
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.).
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Page 282: Index
Index A page number in italics (e.g., 5-26 ) Note indicates an illustration. BACK key function of, 5-8 moving to previous display, 3-11 Aborting a run, 6-20—6-21 selecting diagnostic tests, 7-36 use in directory function, 7-5 ALL history file display option, 7-45, 7-46 use of, 3-11 , 3-16 ALL history file print option, 7-48 Base, See Sample tray...
Page 283 Cleaning the sample block cover, 8-3 Conventions notes and warnings, S-2, P-4 Clear Entry key. See CE key used in manual, S-1, P-3 Condensation. See Loading samples Converting hold times from DNA Thermal CONFIG function. See Configuration function Cycler, 5-4—5-7 Configuration function, 7-16—7-34 Cooling indicator light, 6-16 changing the allowed setpoint error,...
Page 284 setpoints in, 3-3, 4-10, 5-33 Diagnostic function specifying the number of cycles in, 3-18 description of, 7-2 storing, 3-20 See also Diagnostic tests target temperatures in, 3-4 Diagnostic tests, 7-35—7-56 CYCLE print option, 6-14 Chiller Test #3, 7-52—7-53 Heater Test #2, 7-50—7-51 Cycle program.
Page 285 Displayed sample temperature, 10-3 GeneAmp PCR System 9600 Documents on Demand S-19 description of software, 1-5—1-6 Dot-matrix printer. See Printer setup and features of, 1-5 configuration general description of, 1-3 input voltages, 2-4 installing, 2-1—2-21 instrument specifications, 10-1—10-5 Edit function, 5-13 Maintenance, 8-1—8-18...
Page 286 Keypad, 1-4 , 4-2 default value in CYCL program, 5-34 description of, 4-2—4-3 in DNA Thermal Cycler 5-2 types of keys, 4-3 in GeneAmp PCR System 9600, 5-2 HOME option description of, 5-9 use in methods, 5-17 Laboratory requirements, 2-5...
Page 287 use in 96-position sample tray, 6-2 MORE key Main menu, 3-6 function of, 6-11 CREATE option, description of, 4-4 moving between two run-time displays, cursor on, 3-6 3-26, 3-26 , 6-18 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 Offset...
Page 288 PCR programs and methods Printer cable connection, 2-7 overview of, 4-6—4-7 Printer interface, 10-5 setting up, 5-1—5-45 Printer Kit PCR technique for 115VAC printer, 2-6 annealing step, 1-2 for 230VAC printer, 2-10 Denaturing step, 1-2 Printer setup and configuration, 2-6—2-13 description of, 1-2 See also Configuration function Extending step, 1-2...
Page 289 Program numbers data records 7-42 assigning to methods, 5-21 status records, 7-39 assigning, 5-11 Reviewing the history of a run, 6-22 use in creating methods, 5-18, 5-45 RTD probe use in deleting programs, 7-57 description of, 8-5 viewing a directory of programs by, placing in sample wells A1 and A2, 8-14 7-4—7-6, 7-6 placing in sample wells E1 and D1, 8-6...
Page 290 Run-time displays, 6-17— 6-19 Sample tray 96-position Run-time keys, 4-3, 6-11 installing, 6-2, 6-3 Run-time printer mode loading without samples, 3-22—3-23 turning on and off, 7-20 placing in the block, 6-5 , 6-5 turning on, 2-13 removing, 6-8 Sample tray retainer installing, 6-4, 6-4 Sample tube reaction volume, in Sample block cover...
Page 291 default value, 7-26 temperature calibration, 10-5 temperature interval, 7-26, 7-26 Starting a run, 6-11—6-16 SETPOINT print option Starting up the instrument, 3-5 example printout, 6-15 STAT history file display option, 7-45, 7-47 SETPOINT print option, 6-14 STAT history file print option, 7-48 Setpoint time.
Page 292 use in Verify Calibration test, 7-56 Temperature, requirements for installation, Target temperature See also Sample temperature, Setpoints Test # 1. See Reviewing the history file in CYCL programs, 3-4 Test # 2. See Heater test See also Sample temperature Test # 3. See Chiller test Technical support S-14—S-19 E-mail address S-14 Test # 4.
Page 293 Unpacking the instrument, 2-2 Unprotected programs, deleting, 7-61 User diagnostics. See Diagnostic tests 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...
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Page 295 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.
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Applied Biosystems GeneAmp PCR System 9600 User Manual

Table of Contents

Chapter 6. Running PCR Samples

Table of Contents

Chapter 1. Introducing the Geneamp ® PCR System 9600

Chapter 2. Installing the Geneamp PCR System 9600

Chapter 3 Tutorial: Customizing a PCR CYCL Program

Chapter 4. Software Basics

Chapter 5 Setting up PCR Programs and Methods

Chapter 7. Utilities

Chapter 8. Maintenance

Chapter 9. Troubleshooting

Chapter 10. Specifications

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