Applied Biosystems GeneAmp PCR System 9700 User Manual
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Applied Biosystems GeneAmp PCR System 9700 User Manual

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Base Module
P/N N805-0200
User's Manual

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Summary of Contents for Applied Biosystems GeneAmp PCR System 9700

  • Page 1 GeneAmp ® System 9700 Base Module P/N N805-0200 User’s Manual...
  • Page 3 GeneAmp PCR System 9700 ® Base Module User’s Manual...
  • Page 4 Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document.

  • Page 5: Table Of Contents

    GeneAmp PCR System 9700 Labels and Warnings........
  • Page 6 About the GeneAmp PCR System 9700 ........
  • Page 7 Turning the Run-Time Beeper On or Off ........3-9 Setting the Pause Time Out .
  • Page 8 Pausing a Run ............4-8 Stopping a Run Before It Completes .
  • Page 9 Introduction ............5-18 Editing a Method .
  • Page 10 A Instrument Specifications Overview ..............A-1 About This Appendix .
  • Page 11 Damages, Claims, and Returns..........D-3 Damages .

  • Page 13: Introduction And Safety

    This chapter provides information to help you safely operate the GeneAmp System 9700. The following topics are covered in this chapter: In This Chapter Topics See Page About This Manual Instrument Safety Chemical Safety GeneAmp PCR System 9700 Labels and Warnings Laboratory Environmental Requirements 1-11 Introduction and Safety 1-1...

  • Page 14: About This Manual

    About This Manual ® Overview This manual describes how to use the GeneAmp PCR System 9700. It includes the following chapters and appendixes: ♦ Chapter 1, “Introduction and Safety,” contains safety information. ♦ Chapter 2, “Product Overview,” describes the instrument, its components, and requirements for installation.

  • Page 15: Instrument Safety

    Biosystems. Although the instrument has been designed to protect the user, this protection can be impaired if the instrument is used improperly. Five user attention words appear in the text of all Applied Biosystems user Documentation User documentation. Each word implies a particular level of observation or action as Attention Words described below.

  • Page 16: Symbols On Instruments

    Safety Symbols The following is an illustrated glossary of all nonelectrical safety alert symbols found on Applied Biosystems instruments. Each symbol may appear by itself or in combination with text that explains the relevant hazard (see “Safety Labels on Instruments” on page 1-5). These safety symbols may also appear next to DANGERS, WARNINGS, and CAUTIONS that occur in the text of this and other product-support documents.

  • Page 17: Safety Labels On Instruments

    Safety Labels on Instruments The following CAUTION, WARNING, and DANGER statements may be displayed on Applied Biosystems instruments in combination with the safety symbols described in the preceding section. English Francais CAUTION Hazardous chemicals. Read the...

  • Page 18: Chemical Safety

    Comply with all local, state/provincial, or national laws and regulations related to chemical storage, handling, and disposal. Chemical Waste Wastes produced by Applied Biosystems CHEMICAL WASTE HAZARD. Hazard Warning instruments are potentially hazardous and can cause injury, illness, or death.

  • Page 19: About Msdss

    . Be sure to familiarize yourself with the MSDSs CHEMICAL HAZARD before using reagents or solvents. Ordering MSDSs You can obtain from Applied Biosystems the MSDS for any chemical supplied by Applied Biosystems. This service is free and available 24 hours a day. To obtain MSDSs: 1.

  • Page 20: About Waste Disposal

    About Waste As the generator of potentially hazardous waste, it is your responsibility to perform the actions listed below. Disposal ♦ Characterize (by analysis if necessary) the waste generated by the particular applications, reagents, and substrates used in your laboratory. ♦...

  • Page 21: Geneamp Pcr System 9700 Labels And Warnings

    GeneAmp PCR System 9700 Labels and Warnings Instrument Safety Safety labels are located on the instrument. Each safety label has three parts: Labels ♦ A signal word panel, which implies a particular level of observation or action (e.g., or WARNING). If a safety label encompasses multiple hazards, the CAUTION signal word corresponding to the greatest hazard is used.

  • Page 22: Danger Of Burns

    Danger of Burns PHYSICAL INJURY HAZARD. Hot Surface. Use care when working around this area to avoid being burned by hot components. Grounding and The system 9700 must be grounded for protection against electrical shock. Electrical Safety Do not use an adapter to a two-terminal outlet ELECTRICAL HAZARD.

  • Page 23: Laboratory Environmental Requirements

    Laboratory Environmental Requirements Introduction Take the precautions described in this section whenever you operate the system 9700. Read this section before you install the instrument. The instrument should be used according to the instructions provided in this manual. If used otherwise, the protection provided by this instrument may be impaired. Temperature, IMPORTANT This instrument is designed for indoor use.

  • Page 24: • U.s. And Canadian Safety Standards

    Safety and Electromagnetic Compatibility (EMC) Standards This section provides information on: • U.S. and Canadian Safety Standards • Canadian EMC Standard • European Safety and EMC Standards • Australian EMC Standards U.S. and Canadian This instrument has been tested to and complies with standard UL 3101-1, “Safety Requirements for Electrical Equipment for Laboratory Use, Part 1: General Safety Requirements.”...

  • Page 25: Product Overview

    About This Chapter This chapter describes the GeneAmp PCR System 9700, its components, and requirements for installation. The following topics are contained in this chapter: In This Chapter Topic See page About the GeneAmp PCR System 9700 Product Overview 2-1...

  • Page 26: About The Geneamp Pcr System 9700

    About the GeneAmp PCR System 9700 About the The GeneAmp PCR System 9700 is an automated instrument, specifically designed for the amplification of nucleic acids using the Polymerase Chain Reaction (PCR) Instrument process. The user interface consists of a control panel with a full numeric keypad, soft keys, and a graphical display screen that shows the time and temperature profile for each run.

  • Page 27: Using The Keys

    Using the Keys The following table describes the Control Panel keys in the previous figure. Use to... Soft keys (F1-F5) Select the function specified above the key. The function of each key is defined on the display screen above the key, and is redefined as you view different screens. Numeric keys Enter numbers from left to right into a field you highlight.

  • Page 28: Transfer Or Storage Of Methods

    RS485 ports ♦ With a PCMCIA Flash Memory Card Note Upgrade firmware can be ordered from the Applied Biosystems web site or by contacting PCR Technical Support. For more information about upgrading the firmware, see the following. If you are using...

  • Page 29: How The 9700 Differs From The Geneamp Pcr System 9600

    ® How the 9700 Differs The GeneAmp PCR System 9700 differs from the GeneAmp PCR System 9600 in the following ways: from the GeneAmp PCR System 9600 ♦ Reaction volumes of up to 50 µL only can be run and in the “9600 Mode”, as opposed to 100 µL in the GeneAmp PCR System 9600.

  • Page 31: Instrument Setup

    Instrument Setup Overview ® About This Chapter This chapter provides information on how to set up the GeneAmp PCR System 9700 and place it correctly in the laboratory, how to configure the instrument, and how to connect and configure a printer. In This Chapter The following topics are covered in this chapter: Topic...

  • Page 32: Unpacking The Instrument

    To order additional instruments or supplies, contact one of the regional offices listed in Appendix C, “Contacting Services and Support.” You can order modules, accessories, and disposables from Applied Biosystems. Additional Part Numbers To order this part...

  • Page 33: Setting Up Your Laboratory

    Setting Up your Laboratory Choosing a Location To prevent vibration, place the GeneAmp PCR System 9700 on a solid, stable, level surface that allows free airflow overhead and around the sides and back. You should keep all ventilation slots in the instrument cover free of obstruction, for example from excess printer paper.

  • Page 34: Fuse Service Configuration

    The GeneAmp PCR System 9700 will not operate without an interchangeable sample block module installed. For an example, refer to the GeneAmp PCR System 9700 96-Well Sample Block Module User Guide, for instructions on how to install a block and configure the samples.

  • Page 35: Double-Line Fuse

    Double-Line Fuse Introduction FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with listed and certified fuses of the same type and rating as those currently in the instrument. IMPORTANT For proper operation, you must know the power source(s) available and determine if the instrument fuse configuration is correct.

  • Page 36: Turning On The Instrument

    GeneAmp® PCR System 9700 Name:tc001 User:<<pe>> Create Edit Util User Note The Main menu should appear within a few seconds. If any permanent patterns of lines or bars display on the screen, contact Applied Biosystems Technical Support. 3-6 Instrument Setup...

  • Page 37: Setting Custom Parameters

    Setting Custom Parameters Overview The instrument is shipped with default configuration values. The following procedure describes how to set customized values as well as how to enable or disable optional features. Displaying the To display the Configuration Screen: Configuration Step Action Screen From the...

  • Page 38: Setting The Time

    Setting the Time In the first Configuration screen, you can set the current time and date for file memory maintenance, and run-time displays. You can also enable or disable the run-time printer and the run-time beep. To set the time: Step Action Use the Circular Key Pad to select the...

  • Page 39: Turning The Run-Time Beeper On Or Off

    Turning the When turned on, the run-time beeper beeps during a pause and once at the completion of a run. The default value is Off. Run-Time Beeper On or Off To turn the Run Time-Beeper on or off: Step Action Select the field.

  • Page 40: Defining The Idle State Setpoint Temperature

    Baud Rate field. Rate for Your Printer Port Serial Board Specifications You can connect the GeneAmp PCR System 9700 to any printer with a serial interface board and the following specifications. Baud Rate 9600...

  • Page 41: Configuring The Contrast And Screen Saver Options

    IP address and instrument name you select in the following procedure. Note See the System 9700 Networking Software User’s Manual (P/N 4309575) for more information about networking GeneAmp PCR System 9700 instruments. To set the IP Address for an instrument: Step Action Select to display the second configuration screen.
  • Page 42 To set the IP Address for an instrument: (continued) Step Action Using the Circular Key Pad and Enter key, enter up to a 16 character name for identifying the instrument on the network. abcdefghi jklmnopqr stuvwxyz IP Name: Cycler 01 .,-+/():= Press ENTER key to select a character.

  • Page 43: Running Instrument Diagnostics

    Running Instrument Diagnostics Overview The instrument provides a number of internal diagnostic utilities, tests you can run to verify that the instrument hardware and software components meet performance specifications. Viewing the The following procedure describes how to view the Diagnostic screen. Diagnostic Screen To view the Diagnostic screen: Step...

  • Page 44: Testing The Electrical Components

    Testing the Use the hardware diagnostic utilities to test the electrical components of the 9700 instrument. Electrical Components To test the electrical components: Step Action From the screen, press Diagnostics Hard The Hardware Diagnostics appears. Hardware Diagnostics Disp - LCD Display Diagnostic Keypad - Keypad Diagnostic Disp...

  • Page 45: Testing The Display Screen

    Testing the Display The Display diagnostic test allows you to visually determine if the display screen is properly functioning by turning on and off all the LCD pixels. Screen To test the display screen: Step Action From the screen, press Hardware Diagnostics Display The Display Diagnostic screen appears.

  • Page 46: Testing The Keypad

    Testing the Keypad Use the Keypad diagnostic test to verify that all 22 keys on the control panel are functioning properly. To test the keypad: Step Action From the screen, press Hardware Diagnostics Keypad The Keypad Diagnostic screen appears. Keypad Diagnostic After pressing Run, press the blinking key or press STOP twice to exit.

  • Page 47: Using The T Calculator

    Using the T Calculator How to Use the Use the T Calculator to determine the annealing temperature of a primer set of known sequence. Calculator To use the T Calculator: Step Action From the Main menu, press Util . The Utilities screen opens as shown below. Utilities Diag - Instrument diagnostics...

  • Page 48: Upgrading The System Firmware

    Upgrading the System Firmware Introduction You can update the GeneAmp PCR System 9700 firmware from a serial connection to the RS485 port or from a PCMCIA Flash Memory Card. Contact your local Applied Biosystems representative to obtain a PCMCIA Flash Memory Card.
  • Page 49 To upgrade the firmware through the RS485 serial port: (continued) Step Action From the Firmware Upgrade screen, press Serial Serial Port Firmware Upgrade Attach cable from RS485 port on 9700 to serial port on computer. Press Update, then begin download of file from the computer.

  • Page 50: Downloading Firmware Using Windows 95 Or Windows Nt

    Protocol Enter Kermit. A dialog box appears that displays the current packet number and the number remaining. When the download is complete, the GeneAmp PCR System 9700 automatically resets. From the menu, choose to save the parameters.

  • Page 51: Downloading Firmware Using Windows 3.1

    A message at the bottom of the window indicates that the program is sending the file and a progress bar appears. When the download is complete the GeneAmp PCR System 9700 automatically resets. When the download is complete, from the...

  • Page 52: Upgrading Firmware From A Pcmcia Flash Memory Card

    The following procedure describes how to upgrade the firmware using a PCMCIA Flash Memory Card. Firmware from a PCMCIA Flash Contact your local Applied Biosystems representative to obtain a PCMCIA Note Memory Card Flash Memory Card. To upgrade using a PCMCIA Flash Memory Card:...
  • Page 53 To upgrade using a PCMCIA Flash Memory Card: (continued) Step Action If the PCMCIA Flash Memory Card contains a valid firmware upgrade, the Upgrade screen appears. DO NOT TURN OFF THE INSTRUMENT OR REMOVE THE PC CARD! Upgrading the instrument firmware will take approximately 30 seconds.

  • Page 54: Copying Methods

    Copying Methods How to Copy You can copy methods from a Methods Transportability card to the instrument or from the instrument to a Methods Transportability card (P/N 940-1064). Runs can be made Methods directly from methods on a Methods Transportability card. To copy a method: Step Action...
  • Page 55 To copy a method: (continued) Step Action In the Copy Method dialog box, you can take the following action: Press... To... ToInst Transfer a method from a Methods Transportability card to the instrument. ToCard Transfer a method from the instrument to a Methods Transportability card.

  • Page 56: Connecting And Configuring A Printer

    Connecting and Configuring a Printer Connecting a Printer If you connect an optional printer to your 9700 instrument, you can print out a hard copy of the time and temperature parameters for the PCR methods you create. Connect one end of your printer cable (N805-1326) to the RS-485 serial port on the side panel of the 9700 instrument and connect the other end to the RS-232C interface serial adapter on the rear panel of the printer.

  • Page 57: Running Pcr Samples

    Running PCR Samples Overview About This Chapter This chapter provides information on selecting a method, starting and stopping a run, reviewing the history of a run, and what to do when the run is completed. The following topics are covered in this chapter: In This Chapter Topic See page...

  • Page 58: Selecting A Method

    Selecting a Method Introduction After you have prepared your samples and loaded them in the sample block, you can run a PCR amplification with a new or a stored method. What Is a Method A method is a set of instructions in which you specify how the instrument should heat and cool your samples in a PCR thermal profile.

  • Page 59: Selecting A Method

    Selecting a Method If the method you want to run has already been created and stored, you can select it from a list. If the method you want to run has not been created, see Chapter 5, “Creating and Editing Methods.” To select a method: Step Action...

  • Page 60: Viewing Method Parameters

    Viewing Method To view parameters of a method before running: Parameters Step Action From the Stored Methods screen, press View screen appears. The screen shows all the parameters of the View Method method you selected. 2 Hld 3 Tmp 25 Cycles 2 Holds 94.0 94.0...

  • Page 61: Sorting Methods

    Sorting Methods If you have a large number of stored methods, you can sort them by name, date last used, date stored and size. To sort methods: Step Action From the screen, press Stored Methods Sort The sorting criteria screen appears. Sort Methods By: Method name Date last used...

  • Page 62: Running A Method

    Running a Method Starting a Run After choosing a method, follow these steps to start a run. To start a run: Step Action From the menu, press to display stored methods. Main Use the up and down Circular Key Pad to select the method. a.

  • Page 63: About The Run Time Screen

    To start a run: (continued) Step Action Press Start to start a run. If the temperature of the heated cover is less than 103 °C, this message, “Cover is heating” appears. Please wait. Cover is heating Current temperature: 65°C The run will begin when the heated cover reaches 103°C.

  • Page 64: Viewing Method Information

    Viewing Method You can view the Method Information screen during a run by pressing Info. Press Return to return to the Run Time screen. Information 02:32 PM Information 55.2°C User: lisa Method: XL PCR Run started at 01:32:30 PM, 01/01/00. Run will end at 06:35:30 PM, 01/01/00.

  • Page 65: Stopping A Run Before It Completes

    Stopping a Run The following procedure describes how to stop a run before it completes. Before It Completes To stop a run before it completes: Step Action Press the key. Stop screen appears. Stop confirmation Sample 50.1 Confirm Stop Press STOP to abort. Press Resume to continue.

  • Page 66: Reviewing The History Of A Run

    Reviewing the History of a Run How to Review the You can read a record of the events and errors that occurred during a run by reviewing the history file. The instrument stores the history file until it is overwritten by the next History of a Run method used.

  • Page 67: History File Records

    History File Records The following table lists the history file records. Record Description Type History of method xxxxxxxxxxxxxxx This header record is always created. Report User xxxxxx Reaction volume xxx µL Note If you stopped a method before Run started at hh:mm:ss am mm/dd/yy it completed running, then the Run ended at hh:mm:ss am mm/dd/yy message, Run ended at..., will be Run...

  • Page 68: When A Run Completes

    When a Run Completes End of Run Screen At completion of a run, the instrument beeps and the End of Run screen appears. From the End of Run screen you can perform the same functions as you can from the Stop Run screen.

  • Page 69: Creating And Editing Methods

    Creating and Editing Methods Overview About This Chapter This chapter provides information about how to create and edit PCR methods and how to work with stored methods. The following topics are covered in this chapter: In This Chapter Topic See page Adding or Changing Users Creating Methods Modifying Cycling...

  • Page 70: Adding Or Changing Users

    Adding or Changing Users ® Introduction The GeneAmp PCR System 9700 stores methods by user’s names. You can add up to 19 different user names to the instrument. Once you’ve added your name to a list of users, and stored a method under that name, you can run the method at any time by selecting it from the Stored Methods screen (See “Selecting a Method”...

  • Page 71: Protecting Methods

    To add a new user name: (continued) Step Action In the User Name field, enter an alphanumeric name up to six characters in length. You can take the following action: If you want to... Then... select a character in the list shown in use the Circular Key Pads.
  • Page 72 Follow the procedure below to protect a method. To protect a method: Step Action Press PIN # New PIN Number screen appears. Create a PIN Number Your PIN number protects the access to your user name and protection level Enter a PIN number. New PIN #: XXXX Accept Cancel...

  • Page 73: Changing A User Name

    Changing a User If you know the personal identification number for a user name, you can use the Circular Key Pad to select that name, and change it. Name To change a user name: Step Action From the menu, press Main User screen appears.

  • Page 74: Creating Methods

    Creating Methods About the Default The GeneAmp PCR System 9700 comes with a default PCR thermal profile called a method. The create screen displays this default method. For information on displaying Method the create screen, see “Displaying the Create Methods Screen” on page 5-7.

  • Page 75: Displaying The Create Methods Screen

    Displaying the Follow the steps below to display the Create Methods screen. Create Methods To display the Create Methods screen Screen Step Action From the menu, press . The create screen appears. Main Create 1 Hld 3 Tmp 25 Cycles 2 Holds 94.0 94.0 72.0...

  • Page 76: Entering Temperature Control Parameters

    Entering When you enter temperature control parameters, you define values for parameters in each of the three segments of a method: pre-PCR, PCR, and post-PCR. Temperature Control Parameters To enter temperature control parameters: Step Action On the screen, select a field. Create When you first display the Create screen, the field is highlighted.

  • Page 77: Defining Pre-Pcr Holds

    Defining Pre-PCR The Hld field on the Create screen defines the number of holds for the pre-PCR segment of your method. One (1) is the typical setting for most PCR amplifications Holds and is the default value for the Hld field. Generally, pre-PCR holds define a temperature and hold-time sufficient to denature any endonucleases or exonucleases that may contaminate your prepared samples.

  • Page 78: Defining Post-Pcr Holds

    To define the PCR parameters: (continued) Step Action Create the first hold-time parameter: a. Press Enter b. Type in a hold-time value between 00:00 and 98:59 (minutes:seconds). Repeat step 3 and step 4 until you have time and temperature values for each of the segment temperature control parameters you defined in step 1.

  • Page 79: Modifying Cycling

    Modifying Cycling Introduction In addition to customizing values for PCR temperature control parameters, you can use the More function on the create screen and access cycle modification functions that allow you to: ♦ Auto-increment/decrement time and temperature parameters. ♦ Modify up-ramp and down-ramp rates in the cycling segment of a method. ♦...

  • Page 80: Modifying Ramp Rates

    To automatically change temperature control parameters: (continued) Step Action You can take the following action: If you want to... Then press... increase the value every cycle + (plus sign). (a plus sign displays in the current field) decrease the value every cycle - (minus sign).

  • Page 81: Inserting Holds

    To modify ramp rates: (continued) Step Action Modify the up-ramp and down-ramp rates you selected by defining them as a percentage of the maximum of 100%: If you want to... Then press... increase the ramp rate by 10% up to a maximum of 100% key.

  • Page 82: Deleting Holds

    Deleting Holds Follow the procedure below to delete holds. To delete holds: From the screen, select a hold parameter and press Edit More Use the Circular Key Pad to a select a time or temperature hold parameter. 2 Pre-PCR 3 Tmp 25 Cycles 2 Holds 94.0 94.0...
  • Page 83 To insert a programmed pause: (continued) Step Action From the Insert screen, press Pause . The Programmed Pause screen appears. Define Programmed Pause Start first pause at cycle 1 of 25. Pause every 25 cycles for 00:30. Beep during the pause? No Accept Cancel In the...

  • Page 84: Editing Programmed Pauses

    Editing If you have inserted a programmed pause in your method, you can edit the parameters for the pause at any time. Programmed Pauses To edit programmed pauses: Step Action From the screen, use the Circular Key Pad to highlight the word .

  • Page 85: Printing A Method

    To name and store methods: (continued) Step Action In the Method Name field, follow these steps to enter a 1–16 character alphanumeric name. Step Action Use the Circular Key Pad to select a character in the list shown in the upper right portion of the screen.

  • Page 86: Editing Or Deleting Methods

    Editing or Deleting Methods Introduction After you create a method, you can edit its parameters, and store the method by the same name, or change its name. At some time, you may also want to delete a method if you are no longer using it. You can access all editing functions from the Main menu. The delete screen is accessed through the utility menu.
  • Page 87 To edit a method: (continued) Step Action Press Edit after selecting a method. The Edit screen appears. 2 Pre-PCR 3 Tmp 25 Cycles 2 Holds 94.0 94.0 72.0 72.0 55.0 10:00 0:30 55.0 0:30 5:00 2:00 0:30 Hold Cycle Pause Cancel Choose a temperature or time parameter within a PCR segment.

  • Page 88: Deleting A Method

    Deleting a Method The following procedure describes how to delete a method. To delete a method: Step Action From the screen, press and then press . The Delete Method Utilities More Delete screen appears. Delete Method Methods on Inst User Size Stored exp001...
  • Page 89 To delete a method: (continued) Step Action Press to confirm the deletion. This deletes the method and returns you to the Delete screen. Note Even after you delete the last method stored under a User name, the name is removed from the instrument. To delete the name, see “Deleting a User Name” on page 5-5.

  • Page 91: Converting Hold Times

    Converting Hold Times Overview ® About This Chapter This chapter provides information about setting hold times for the GeneAmp System 9700 compared to the DNA Thermal Cycler or DNA Thermal Cycler 480. This information is based upon differences in how the instruments heat and cool samples. Note Protocols using sample volumes between 5 µL and 50 µL, developed on either the ®...

  • Page 92: About Setting Hold Times

    A hold time of one minute or greater is required on the DNA Thermal Cycler and the DNA Thermal Cycler 480 for samples to reach the target temperature. On the GeneAmp PCR System 9700, hold times of less than one minute are generally used.

  • Page 93: Guidelines For Converting Hold Times

    Subtract the number of seconds indicated from the hold time used for the DNA Thermal Cycler or the DNA Thermal Cycler 480. The result is the hold time to use for the GeneAmp PCR System 9700. Note The typical hold time is 10 to 15 seconds for denaturation.

  • Page 94: Up Ramp Example

    35 seconds (see the figure below). Note If methods developed on the GeneAmp PCR System 9700 will be used on the DNA Thermal Cycler or the DNA Thermal Cycler 480, you can also use Table 6-1 to convert the hold times.

  • Page 95: Table Of Conversions

    Thermal Cycler 480, resulting in a new hold time of 27 seconds. Note If the methods developed on the GeneAmp PCR System 9700 will be used on the DNA Thermal Cycler or the DNA Thermal Cycler 480, use Table 6-2 to convert the hold times. Add the indicated times instead of subtracting them.

  • Page 97: Routine Maintenance

    System 9700. ELECTRICAL SHOCK HAZARD. Severe electrical shock can result from operating the GeneAmp PCR System 9700 Base Module without its instrument panels in place. Do not remove instrument panels. High-voltage contacts are exposed when instrument panels are removed from the instrument.

  • Page 98: Changing The External Fuses

    Changing the External Fuses Introduction FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with Listed and Certified fuses of the same type and rating as those currently in the instrument. All instruments have factory installed fuses. However, if you should ever need to change a fuse, follow the instructions in “Changing the External Fuses”...

  • Page 99: Changing Fuses

    Changing Fuses Instruments have two 8 amp Type T 250 V 5x20 mm fuses ( P/N 0999-1683). To change the fuses: Step Action Turn off the instrument and disconnect the power cord from the side of the instrument. ELECTRICAL SHOCK HAZARD. Severe electrical shock, which could cause physical injury or death, can result from working on an instrument when the high voltage power supply is operating.

  • Page 101: Troubleshooting

    Troubleshooting Overview About This Chapter This chapter describes instrument problems you may have, the probable causes of these problems, and any display screen messages you may encounter when using ® the GeneAmp PCR System 9700. In This Chapter The following topics are covered in this chapter: Topic See page If There Is a Power Failure...

  • Page 102: If There Is A Power Failure

    If There Is a Power Failure Introduction An automated restart function allows for power failures and safe continuation of a PCR run after resumption of power. During a Power The following table lists the actions the instrument takes if the power is interrupted and the instrument turns off while you are operating it.

  • Page 103: Display Screen Error Messages

    Display Screen Error Messages Error Messages Refer to the following table for a description of error messages, and recommended actions that you should take. Table Table 8-1 Error Messages Message Description Recommended Action Battery RAM version number This error is generated when the battery RAM has Call Technical Support.
  • Page 104 The feature is not implemented in the current firmware Upgrade firmware when the version. new version is available from Applied Biosystems. PC card and Flash do not The PC (upgrade) card and instrument memory do not Call Technical Support. verify match.
  • Page 105 Table 8-1 Error Messages (continued) Message Description Recommended Action Preferences battery RAM User configuration has been reset due to software Call Technical Support. initialized error. Printer not responding The printer has been disconnected or is off line. Check printer connections and power switch.

  • Page 106: Troubleshooting Information

    Heated cover failure. Call Technical Support. ♦ Heating rate too slow Peltier failure. Run Rate Test diagnostic. Call Applied Biosystems Technical Support. ♦ Ambient temperature is too warm. ♦ Run Rate Test diagnostic. Instrument can’t reach high or low temperature range ♦...

  • Page 107: A Instrument Specifications

    Instrument Specifications Overview About This This appendix describes the dimensions, power, and electrical specifications for the ® GeneAmp PCR System 9700 system, including the control panel, sample Appendix temperature information, and printer specifications. In This Appendix The following topics are covered in this appendix: Topic See page System Specifications...

  • Page 108: System Specifications

    System Specifications Dimensions The following tables list the footprint and the weight of the instrument with the 96–Well or 60–Well sample block module. Footprint (With Sample Block Module Installed) Height 26 cm (10 in) Width 28 cm (11 in) Depth 41 cm (16 in) Note You must provide sufficient space around the instrument for unrestricted air circulation.
  • Page 109 Amperage (A) Location Voltage (VAC) Frequency Nominal Japan 220 ±10% 50/60 Hz ±1% 3.16 USA/Canada 120 ±10% 50/60 Hz ±1% 4.20 Europe (pre-1992) 220 ±10% 50/60 Hz ±1% 3.16 230 ±10% 50/60 Hz ±1% 3.14 UK (pre-1992) 240 +6%/–10% 50/60 Hz ±1% 3.12 Australia 240 +6%/–10%...

  • Page 110: Control Panel Specifications

    Control Panel Specifications Display Screen The display screen is a 7 x 40 character display with a graphics mode of 60 x 240 pixel resolution. Keys The instrument control panel consists of a display screen and 22 keys. The keys are: ♦...

  • Page 111: B Supplied Methods

    Supplied Methods Overview About this Appendix This appendix provides information about the methods that are supplied with the ® GeneAmp PCR System 9700. The following topics are covered in this appendix: In This Appendix Topic See page About the Methods AmpliCycle Sequencing AmpliTaq Gold DNA Polymerase BigDye Terminators...

  • Page 112: About The Methods

    About the Methods Introduction The instrument supplies you with eight pre-coded methods stored under the user name <<pe>>. The eight pre-coded methods are: ♦ AmpliCycle ® Sequencing ♦ ® AmpliTaq Gold DNA Polymerase ♦ ® BigDye Terminators ♦ General PCR ♦...

  • Page 113: Bigdye Terminators

    RISM ® ® terminator sequencing using ABI P BigDye Terminator Cycle Sequencing Ready Reaction Kits (available from Applied Biosystems). It consists of 25-cycle, three-temperature cycle sequencing followed by an infinite hold at 4 °C. 3 Tmp 25 Cycles 1 Hld 96.0 60.0...

  • Page 114: Lms2

    LMS2 The GeneAmp PCR System 9700 software includes a pre-coded LMS2 method for RISM ® ABI P Linkage Mapping Set Version 2 (LMS2) thermal cycling. Linkage Mapping Set 2 employs over 400 fluorescent-labeled PCR primer pairs for analysis of select microsatalite loci from the Généthon human linkage map.

  • Page 115: Touchdown Pcr

    Touchdown PCR When the optimal annealing temperature is unknown, one strategy, touchdown PCR, incrementally decreases the annealing temperature in early cycles in order to maximize the yield of specific products. 2 Tmp x 20 2 Tmp x 10 94.0 94.0 0:15 0:15 65.0...

  • Page 117: C Contacting Services And Support

    • Obtain information about customer training • Download software updates and patches In addition, the Services and Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities. Contacting Services and Support C-1...

  • Page 119: D Limited Warranty Statement

    Applied Biosystems will repair or replace, at its discretion, defective accessories during this warranty period. After this warranty period, Applied Biosystems will pass on to the buyer, to the extent that it is permitted to do so, the warranty of the original manufacturer for such accessories.
  • Page 120 Applied Biosystems warrants that for a period of ninety (90) days from the date the warranty period begins, the tapes, diskettes, or other media bearing the operating software of the product, if any, will be free of defects in materials and workmanship under normal use.

  • Page 121: Damages, Claims, And Returns

    Damages If shipping damage to the product is discovered, contact the shipping carrier and request inspection by a local agent. Secure a written report of the findings to support any claim. Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a Return Authorization (RA) number.
  • Page 123 Index cycles Numerics counting of 4-7 480 DNA Thermal Cycler inserting 5-14 converting hold times 6-2 to 6-5 cycling, modifying 5-11 to 5-17 AutoX function, using 5-11 to 5-12 cycles, inserting 5-14 alphanumeric characters, entering 5-3 deleting holds 5-14 AmpliCycle Sequencing 4-2, B-2 holds about supplied method B-1, B-2, B-3 inserting 5-13...
  • Page 124 1-9 heated cover screen 4-7 GeneAmp PCR System 9700 heating, of samples 5-8 Control Panel history of run, reviewing about 2-2 history file records 4-11 specifications A-4 history formats 4-10 copying methods 3-24 to 3-25 procedure 4-10 custom parameters, setting 3-7 to 3-11...
  • Page 125 temperature control parameters, entering 5-8 pauses, programmed editing or deleting methods 5-18 to 5-21 editing 5-16 modifying cycling 5-11 to 5-17 inserting 5-14 AutoX function, using 5-11 to 5-12 PCMCIA card cycles, inserting 5-14 using to copy methods 3-24 to 3-25 deleting holds 5-14 using to upgrade firmware 3-22, 3-23 naming and storing methods 5-16 to 5-17...
  • Page 126 Sort, function of 4-5, 5-20 chemical hazard 1-6 SRAM card, using to copy methods 3-24 to 3-25 chemical waste hazard 1-6 starting instrument 3-6 warranty stop bit 3-10, 3-26 damages, claims, returns D-3 Stop key, definition of 2-3 exceptions D-2 storing methods 5-16 to 5-17 for computers with altered configuration D-1 system firmware, upgrading 3-18 to 3-23...
  • Page 128 Toll Free (In North America): +1 800.345.5224 Fax: +1 650.638.5884 Worldwide Sales and Support Applied Biosystems vast distribution and service network, composed of highly trained support and applications personnel, reaches 150 countries on six continents. For sales office locations and technical support, please call our local office or refer to our Web site at www.appliedbiosystems.com.

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