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Supplied Methods B-1

Supplied Methods

Overview

About this Appendix

This appendix provides information about the methods that are supplied with the
GeneAmp

PCR System 9700.

In This Appendix

The following topics are covered in this appendix:

Topic

See page

About the Methods

B-2

AmpliCycle Sequencing

Summary of Contents for GeneAmp PCR System 9700

Page 1: ...GeneAmp PCR System 9700 Base Module User s Manual ...

Page 2: ...onent of that license may be purchased from Applied Biosystems or obtained by purchasing Authorized Reagents This instrument is also an Authorized Thermal Cycler for use with applications licenses available from Applied Biosystems Its use with Authorized Reagents also provides a limited PCR license in accordance with the label rights accompanying such reagents Purchase of this product does not its...

Page 3: ... Waste Disposal 1 8 GeneAmp PCR System 9700 Labels and Warnings 1 9 Instrument Safety Labels 1 9 Instrument Warnings Diagram 1 9 Danger of Burns 1 10 Electrical Shock Hazard 1 10 Fire Hazard 1 11 Grounding and Electrical Safety 1 11 Fuses 1 11 Laboratory Environmental Requirements 1 12 Introduction 1 12 Temperature Humidity and Environment 1 12 Pollution 1 12 Emission Immunity Statement 1 12 Routi...

Page 4: ...ir Vents 3 3 Fuse Service Configuration 3 4 Input Voltage 3 4 Interchangeable Sample Block Modules 3 4 Converting from a Single to Double Line Fuse 3 5 Introduction 3 5 Fuse Part Number 3 5 Power Entry Module Diagram 3 5 Converting Single to Double line Fuse 3 6 Turning On the Instrument 3 7 Turning On the Instrument 3 7 Setting Custom Parameters 3 8 Overview 3 8 Displaying the Configuration Scree...

Page 5: ... a PCMCIA Flash Memory Card 3 23 Copying Methods 3 25 How to Copy Methods 3 25 Connecting and Configuring a Printer 3 27 Connecting a Printer 3 27 Configuring the Printer 3 27 4 Running PCR Samples Overview 4 1 About This Chapter 4 1 In This Chapter 4 1 Selecting a Method 4 2 Introduction 4 2 What Is a Method 4 2 Predefined Methods 4 2 Selecting a Method 4 3 Viewing Method Parameters 4 4 Searching...

Page 6: ...rs 5 6 Displaying the Create Methods Screen 5 7 Entering Temperature Control Parameters 5 8 Defining Pre PCR Holds 5 9 Defining PCR Parameters 5 9 Defining Post PCR Holds 5 10 Modifying Cycling 5 11 Introduction 5 11 Changing Temperature Control Parameters 5 11 Modifying Ramp Rates 5 12 Inserting Holds 5 13 Deleting Holds 5 14 Inserting Cycles 5 14 Inserting Programmed Pauses 5 14 Editing Programm...

Page 7: ...Conversions 6 5 Down Ramp Example 6 5 7 Routine Maintenance Overview 7 1 About This Chapter 7 1 In This Chapter 7 1 Changing the External Fuses 7 2 Introduction 7 2 Power Entry Module Diagram 7 2 Changing Fuses for Single Line Operation 7 3 Changing Fuses for Double Line Operation 7 4 8 Troubleshooting Overview 8 1 About This Chapter 8 1 In This Chapter 8 1 If There Is a Power Failure 8 2 Introduc...

Page 8: ...ds Overview B 1 About this Appendix B 1 In This Appendix B 1 About the Methods B 2 Introduction B 2 AmpliCycle Sequencing B 2 AmpliTaq Gold B 2 BigDye B 3 General PCR B 3 LMS2 B 4 Time Release PCR B 4 Touchdown PCR B 5 XL PCR B 5 C Contacting Technical Support Technical Support C 1 Contacting Technical Support C 1 To Contact Technical Support by E Mail C 1 To Contact Technical Support by Telephone...

Page 9: ...ix To Obtain Customer Training Information C 7 D Limited Warranty Statement Index ...

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Page 11: ... information to help you safely operate the GeneAmpâ PCR System 9700 In This Chapter The following topics are covered in this chapter Topics See Page About This Manual 1 2 Instrument Safety 1 3 Chemical Safety 1 6 GeneAmp PCR System 9700 Labels and Warnings 1 9 Laboratory Environmental Requirements 1 12 ...

Page 12: ... create and edit PCR methods and how to work with stored methods Chapter 6 Converting Hold Times provides information about setting hold times for the GeneAmp PCR System 9700 compared to the DNA Thermal Cycler or DNA Thermal Cycler 480 Chapter 7 Routine Maintenance provides procedures for routine maintenance on the instrument Chapter 8 Troubleshooting lists error messages and suggestions for deali...

Page 13: ...rds Five user attention words appear in the text of all Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Calls attention to useful information IMPORTANT Indicates information that is necessary for proper instrument operation Indicates a potentially hazardous situation which if not avoided may result in minor or moderate inj...

Page 14: ...h This symbol indicates that a terminal may be connected to another instrument s signal ground reference This is not a protected ground terminal This symbol indicates that this is a protective grounding terminal that must be connected to earth ground before any other electrical connections are made to the instrument A terminal marked with this symbol either receives or delivers alternating current...

Page 15: ...sary of all nonelectrical safety alert symbols found on Applied Biosystems instruments This symbol illustrates a heater hazard Proceed with caution when working around these areas to avoid being burned by hot components This symbol indicates that a laser is present inside the instrument ...

Page 16: ...l local state provincial or national laws and regulations related to chemical storage handling and disposal Chemical Waste Hazard Warning CHEMICAL WASTE HAZARD Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury illness or death Read and understand the material safety data sheets MSDSs provided by the manufacturers of the chemicals in the waste containe...

Page 17: ...tion below For chemicals not manufactured or distributed by Applied Biosystems call the chemical manufacturer WARNING To order documents by automated telephone service 1 From the U S or Canada dial 1 800 487 6809 or from outside the U S and Canada dial 1 858 712 0317 2 Follow the voice instructions to order documents for delivery by fax Note There is a limit of five documents per fax request To or...

Page 18: ... generated by the particular applications reagents and substrates used in your laboratory Ensure the health and safety of all personnel in your laboratory Ensure that the instrument waste is stored transferred transported and disposed of according to all local state provincial or national regulations Note Radioactive or biohazardous materials may require special handling and disposal limitations m...

Page 19: ... located on the GeneAmp PCR System 9700 GR1069 Laboratory Use Electrical Equipment 3Z77 US LISTED N2284 GeneAmp PCR System 9700 Part No Serial No Made in Singapore Warning To reduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel Warning Grounding circuit continuity i...

Page 20: ... The three pronged power cord and receptacle contain the grounding connector ELECTRICAL HAZARD Grounding circuit continuity is vital for safe operation of equipment Never operate equipment with grounding conductor disconnected 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 ope...

Page 21: ...t Grounding and Electrical Safety The system 9700 must be grounded for protection against electrical shock ELECTRICAL HAZARD Do not use an adapter to a two terminal outlet since this does not provide positive ground protection Fuses Improper fuses can damage the wiring system and cause a fire ELECTRICAL FIRE HAZARD Before turning on the instrument verify that the fuses are properly installed WARNI...

Page 22: ...e to potentially explosive materials or objects IMPORTANT The instrument should be stored between 20 C and 60 C 4 F and 140 F at altitudes between 0 and 12 000 meters Note This instrument is able to withstand transient overvoltage according to Installation Category II as defined in IEC 1010 1 Pollution The installation category overvoltage category for this instrument is II and it is classified as...

Page 23: ...rview About This Chapter This chapter describes the GeneAmp PCR System 9700 its components and requirements for installation In This Chapter The following topics are contained in this chapter Topic See page About the GeneAmp PCR System 9700 2 2 ...

Page 24: ...he time and temperature profile for each run Control Panel The instrument control panel consists of a display screen and 22 keys The display screen shows a graphical representation of PCR events including pre PCR holds PCR cycling and post PCR holds You use the keys to enter information into fields on the display screen Control Panel Diagram The following diagram shows the control panel F1 F2 F3 F...

Page 25: ...into a field and advance the highlight box to the next field on a screen Clear Entry key CE Remove information from a field Circular Key Pad Move the highlight box to different fields on the display screen in the direction of the arrow If you want to Then move the highlight box in one of four directions Use the Circular Key Pad advance the box to the next field Press the Enter key Parameter Descri...

Page 26: ...m the Applied Biosystems web site or by contacting PCR Technical Support For more information about upgrading the firmware see the following Use To See Methods Storage Card Centennial 256kb SRAM P N 0940 1064 transfer methods from the Methods Storage card to the instrument or from the instrument to the card for storage Copying Methods on page 3 25 If you are using See a serial cable connection RS4...

Page 27: ...own methods Hold Cycle and Auto programs no longer exist as menu items under the Create function Instead of linking programs together to create a method you create a single method on the GeneAmp PCR System 9700 If the allowed pause time elapses during a manual pause of a method the method will continue running instead of stopping The last method run cannot be re run or edited unless it is first sa...

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Page 29: ...ct and configure a printer In This Chapter The following topics are covered in this chapter Topic See page Unpacking the Instrument 3 2 Setting Up your Laboratory 3 3 Converting from a Single to Double Line Fuse 3 5 Turning On the Instrument 3 7 Setting Custom Parameters 3 8 Running Instrument Diagnostics 3 14 Using the Tm Calculator 3 18 Upgrading the System Firmware 3 19 Copying Methods 3 25 Con...

Page 30: ...n Appendix C Contacting Technical Support Additional Part Numbers You can order modules accessories and disposables from Applied Biosystems Note See the Interchangeable Sample Block Module Users Manual for part numbers of disposable items To order this part Use P N GeneAmp PCR System 9700 Base Module N805 0200 60 Well 0 5 mL Sample Block Module 4309131 Auto Lid Sample Block Module 4312904 96 Well ...

Page 31: ...it and the ambient relative humidity is 20 to 80 What to Avoid When setting up the instrument avoid Placing the instrument under overhanging shelves especially when there is a wall behind the unit Proximity to other instruments on the same bench or other heat generating equipment Locations subject to wide temperature fluctuation such as direct sunlight or air drafts Damp areas Environments where t...

Page 32: ...te fuse configuration based on the voltage used Note The Volt Amp number for this instrument is 725 Volt Amps Interchangeable Sample Block Modules The instrument features an interchangeable sample block module allowing portability and versatility in sample configuration Note The GeneAmp PCR System 9700 will not operate without an interchangeable sample block module installed For an example refer t...

Page 33: ...ne configuration to double line service 220 230 240 V nominals only IMPORTANT For proper operation you must know the power source s available and determine if the instrument fuse configuration is correct The instrument is shipped configured for single line operation Fuse Part Number The correct fuse is an 8 amp Type T 250 V 5x20 mm fuse P N 0999 1683 Power Entry Module Diagram The following is a d...

Page 34: ...supply is operating To avoid electrical shock disconnect the power supply to the instrument unplug the power cord and wait at least 1 minute before working on the instrument 2 Insert a fine flat tip screwdriver into the slot in the upper portion of the power entry module and open the door 3 Pull the fuse compartment out Note Observe the orientation of the metal bars that run from the fuse compartm...

Page 35: ...al seconds the Main menu appears You can use any of the functions displayed above the soft keys 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 F1 F3 F4 F5 F2 APPLIED BIOSYSTEMS www appliedbiosystems com Applied Biosystems F1 F3 F4 F5 F2 GeneAmp PCR System 9700 Copyright 1996 08 00 A...

Page 36: ...tilities screen you can take the following action 2 Press Config The first Configuration screen appears Utilities Diag Instrument diagnostics TmCalc Calculates melting temp Config Instrument configuration F1 F3 F4 F5 F2 Diag Exit More Config TmCalc If you want to See page Delete a method 5 20 Run instrument diagnostics 3 14 Review the history of a run 4 10 Access the Tm calculator 3 18 Copy method...

Page 37: ...current time displays in the Time field 3 Use the numeric keys to type in the hours followed by minutes 4 Press Accept when your entries are complete Note CE clears an entry To set the date Step Action 1 Use the circular key to select the Date field 2 The three fields to set in the Date field are the Days field Month field Year field 3 Press the D M Y or Y M D soft keys until the format you want f...

Page 38: ...ld This changes the value of the soft keys 2 You can take the following action 3 Press Enter to accept your entry If you want to Then turn the beeper on Press ON turn the beeper off Press Off To set the pause time out Step Action 1 Select More to display the second configuration screen 2 Set the Pause Time Out field by using the numeric keys to enter a time in minutes and seconds From this screen ...

Page 39: ... to define the printer port value in the Baud Rate field Serial Board Specifications You can connect the GeneAmp PCR System 9700 to any printer with a serial interface board and the following specifications How to Set the Baud Rates To define the Idle State Set Point temperature Step Action 1 Select the Idle State Set Point field 2 Use the numeric keys and type in a temperature between 4 0 C and 9...

Page 40: ...om the network under the 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 Use This Option To Activate the Screen Saver Smart After 15 minutes unless a method is running Always After 15 minutes Never Never To set the IP Address for an i...

Page 41: ...e the Circular Key Pad to select the last IP field 8 Set the IP field by using the numeric keys to enter an IP address for the instrument 9 Press Accept when all information on this screen is correct To set the IP Address for an instrument continued Step Action abcdefghi Press ENTER key to select a character IP Name Cycler 01 F1 F3 F4 F5 F2 Accept Cancel Back sp jklmnopqr stuvwxyz Instrument Confi...

Page 42: ...on F1 F3 F4 F5 F2 Diag Exit More Config TmCalc Diagnostics Hard Hardware Diagnostics System System Performance Tests TmpVer Temperature Verification Upgrad Firmware Upgrade F1 F3 F4 F5 F2 Hard Exit Upgrad TmpVer System Press this soft key To Hard Access hardware diagnostic utilities that allow you to test hardware and electrical components such as the Display screen and Keypad System Access the sy...

Page 43: ...press Hard The Hardware Diagnostics appears 2 Use the corresponding soft key to select the hardware component for which you want to perform one of the following tasks Hardware Diagnostics Disp LCD Display Diagnostic Keypad Keypad Diagnostic F1 F3 F4 F5 F2 Exit Keypad Disp Press this soft key To Display Visually determine if the Liquid Crystal Display LCD screen is functioning properly Keypad Verif...

Page 44: ...lay screen Step Action 1 From the Hardware Diagnostics screen press Display The Display Diagnostic screen appears 2 You can take the following action Display Diagnostics 1 Read all instructions first 2 Press Run to turn ON all pixels 3 Press STOP to turn OFF all pixels 4 Press STOP to exit F1 F3 F4 F5 F2 Run Exit Press To Run Turn ON all pixels Check display Stop Turn OFF all pixels Check display ...

Page 45: ...ypad Step Action 1 From the Hardware Diagnostics screen press Keypad The Keypad Diagnostic screen appears 2 Press Run The Control Panel screen appears 3 Press the indicated flashing key Keypad Diagnostic After pressing Run press the blinking key or press STOP twice to exit F1 F3 F4 F5 F2 Run Exit ENTER STOP F1 F2 F3 F4 F5 1 2 3 4 5 6 7 8 9 0 CE F1 F3 F4 F5 F2 ...

Page 46: ...000 4 Enter the primer concentration Note The default it 0 20 Enter values 0 01 to 10 00 5 Enter primer sequence in P1 6 Enter primer sequence in P2 and press Enter to calculate the Tms The melting points are displayed Use this information to program a run For more information see Chapter 5 Creating and Editing Methods 7 Press Return to display the Utilities screen Utilities Diag Instrument diagno...

Page 47: ... To upgrade the firmware through the RS485 serial port Step Action 1 Connect the appropriate communication cable from a computer to the RS485 port on the 9700 instrument Base Module see the figure below You can use the following cables For information on connecting the printer cable see page 3 27 2 From the Diagnostics screen press Upgrade The Firmware Upgrade screen appears Communication cable Pa...

Page 48: ...rmware Upgrade F1 F3 F4 F5 F2 Exit Update Attach cable from RS485 port on 9700 to serial port on computer Press Update then begin download of file from the computer DO NOT TURN OFF THE INSTRUMENT OR REMOVE SERIAL CABLE Upgrading over the serial port will take approximately 10 minutes Instrument will re boot when complete F1 F3 F4 F5 F2 If you are using See Microsoft Windows 95 or Microsoft Windows...

Page 49: ...ending on whether you chose Com 1 or Com 2 in the previous step in the Properties dialog box enter the following When you have competed entering the information click OK 6 From the Transfer menu choose Send file The Send File dialog box appears 7 In the Send File dialog box enter the following and click Send A dialog box appears that displays the current packet number and the number remaining When...

Page 50: ... OK 6 From the Send Binary File menu choose Transfers A directory dialog box appears 7 From the directory dialog box find and select the 9700 upgrade file and click OK 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 8 When the download is complete from the ...

Page 51: ...ot at the rear of the right side of the instrument Note The label and arrow on the card face forward and toward the instrument 2 Press the card firmly to ensure the card is seated in the slot IMPORTANT Do not remove the card or turn off the instrument until the upgrade is completed 3 From the Diagnostics screen press Upgrade 4 From the Diagnostics screen press PCcard 5 The Checksum screen appears ...

Page 52: ...ey in the lower right corner brings up the Main menu with the new revision number of the software listed on the screen 7 Remove the PCMCIA Flash Memory Card after you have successfully upgraded the firmware To upgrade using a PCMCIA Flash Memory Card continued Step Action DO NOT TURN OFF THE INSTRUMENT OR REMOVE THE PC CARD Upgrading the instrument firmware will take approximately 30 seconds Instr...

Page 53: ...are into the slot at the rear of the right side of the instrument Note The label and arrow on the card face forward and toward the instrument 2 Press the card firmly to ensure the card is seated in the slot IMPORTANT Do not remove the card or turn off the instrument until the upgrade is completed 3 From the Utilities screen press More and from this secondary utility screen press Copy The Copy Meth...

Page 54: ... the method has been successfully copied To copy a method continued Step 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 Methods on Inst XL PCR Touchdown PCR AmpliTaq Gold AmpliCycle Seq User pe pe pe pe F1 F3 F4 F5 F2 Copy Cancel Sort User View Size 11 6 9 8 Stored 9 9 9...

Page 55: ...e 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 Configuring the Printer After you have connected the printer cable to the printer you must configure the instrument for the printer You can connect the 9700 instrument to any printer with a serial board and the following specifications See your printer manual for i...

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Page 57: ... history of a run and what to do when the run is completed In This Chapter The following topics are covered in this chapter Note For information on loading and unloading samples see the instructions accompanying your interchangeable sample block module Topic See page Selecting a Method 4 2 Running a Method 4 6 Reviewing the History of a Run 4 10 When a Run Completes 4 12 ...

Page 58: ...ofile Methods are stored in the instrument software Predefined Methods The GeneAmp PCR System 9700 supplies eight predefined methods that you can run AmpliCycle Sequencing AmpliTaq Gold BigDye General PCR LSM2 Time Release PCR Touchdown PCR XL PCR Each of these methods is stored under the user name pe You can edit these methods and store them under a different name a different user name or select ...

Page 59: ...he instrument If you need help deciding which method to select you can View method parameters Sort methods by different categories Search for a method by user name 3 Select a method by using the Circular Key Pad to move the highlight box to a method listed on the Stored Methods screen Note You can use the up and down keys as repeat keys for quick scrolling 4 The top line of the display continuousl...

Page 60: ...screen Note You cannot edit parameters from the View Method screen 2 Hld 3 Tmp 25 Cycles 2 Holds 55 0 94 0 2 00 10 00 55 0 0 30 72 0 0 30 72 0 5 00 4 0 94 0 0 30 Start Return Method exp 001 F1 F3 F4 F5 F2 To search for a method Step Action 1 From the Stored Methods screen press User Select which user s methods to view by taking the following action Note You cannot add delete or modify a user name ...

Page 61: ...he displayed methods are sorted according to your selection in step 2 Sort Methods By Method name Date last used Date stored Method size F1 F3 F4 F5 F2 Accept Cancel Choose this item To sort Method name Methods alphabetically Date last used Methods chronologically in descending order by date of use The last method which ran or was stored is listed first Date stored Note Uses the most recent title ...

Page 62: ...the Reaction Volume field The reaction volume range is dependent on the mode selected Note Each method remembers the reaction volume Press the CE key to clear an entry 96 Well Gold Sample Block Module Select 9600 or MAX mode first and then select volume 96 Well Aluminum Sample Block Module Select 9600 or STD mode first and then select volume Select Method Options Enter a value from 5 to 50 µL Reac...

Page 63: ... C Please wait Cover is heating F1 F3 F4 F5 F2 Cancel Sample 56 7 Cycle 1 of 25 HOT 55 0 94 0 2 00 10 00 55 0 0 30 72 0 0 30 72 0 5 00 4 0 94 0 0 30 F1 F3 F4 F5 F2 Pause Info Use the Run Time screen for For more information see page Viewing Method Information 4 8 Pausing a Run 4 8 Stopping a Run Before It Completes 4 9 Pre PCR segment PCR segment Post PCR segment Calculated sample temperature upda...

Page 64: ... a reagent Do not to touch the sample block or the bottom of the heated cover during a pause Figure 4 1 Pause screen Your samples remain at the temperature of the instrument when you pause the run The time remaining in a pause appears at the bottom of the screen in minutes seconds format It decrements to zero and the paused run resumes at the point where you paused it 02 32 PM Information 55 2 C U...

Page 65: ...times are configured by setting the Pause Time Out See Setting the Pause Time Out on page 3 10 2 Press the Stop key again This stops the run and the End of Run screen appears If any errors occur during a run the following message appears Exception occurred check history file Press HIST to review the history file 3 Press Exit to return to the Main menu Sample 50 1 Confirm Stop HOT Press STOP to abo...

Page 66: ...o display the History File screen From the Utilities screen press More and then press Hist From the End of Run screen press Hist 2 Press PageUp to move up through the record or PageDn to move down 3 Press Print to print the record History of method exp002 User lisa Reaction volume 50 µL Run started at 02 30 45 PM 01 01 00 Run aborted at 02 50 42 PM 01 01 00 No exceptions Length of run 00 19 57 Ram...

Page 67: ...mperature drifted x x c from setpt Block drift error The block has drifted 2 C from set point during the hold segment of a run Report Cover error in Cycle xx Setpt xx Repxx Heated cover at xx x c Heated cover drift error The cover has drifted 5 C from 105 C anytime during the run Report Sensor error in Cycle xx Setpt xx Repxx Block sensor failure Block sensor failure Fatal error Call for service S...

Page 68: ...n screen before storing the method the Method Not Stored screen displays The following table lists the actions you can take 11 30 AM 25 1 C Method XL PCR Run completed at 11 30 05 AM 01 01 00 Length of run is 01 34 25 End of Run F1 F3 F4 F5 F2 Hist Exit If you Then press want to store the method Store do not want to store the method Exit Note The Method Not Stored screen appears for a few seconds ...

Page 69: ...provides information about how to create and edit PCR methods and how to work with stored methods In This Chapter The following topics are covered in this chapter Topic See page Adding or Changing Users 5 2 Creating Methods 5 6 Modifying Cycling 5 11 Printing a Method 5 17 Editing or Deleting Methods 5 18 ...

Page 70: ...ecomes the current user name All new methods that you create are stored by default under the current user name Adding a New User Name You add a new user name by entering an alphanumeric name on the User Name screen To add a new user name Step Action 1 From the Main menu press User The Select User Name screen appears A list of names of all users who have been added to the instrument displays in a 4...

Page 71: ...in the upper right portions of the screen use the Circular Key Pads put the alphabetic character in the User Name field press Enter enter the numbers directly into the User Name field use the numeric keys go back one space and remove a single character hold down the Soft key and go back multiple spaces If you Then do not want to protect your method press Accept again want to protect your method se...

Page 72: ...pt when you have entered a PIN you want to keep The Select User Name screen appears The new name you entered should now display on the screen Press Cancel to cancel your entry and return to the previous screen Create a PIN Number F1 F3 F4 F5 F2 Accept Cancel Your PIN number protects the access to your user name and protection level Enter a PIN number New PIN XXXX Confirm PIN Number F1 F3 F4 F5 F2 ...

Page 73: ...se the Circular Key Pad to select the name you want to change 3 Press Edit If a PIN has been previously entered the Security Check screen appears 4 Type in the four digit PIN of the user name you selected 5 Press Name to enter a new user name 6 Press the CE key to clear the previous name 7 Enter a new user name 8 Press Accept The Security Code screen appears again To delete a user name Step Action...

Page 74: ...ture Control Parameters Pre PCR Holds PCR Parameters Post PCR Holds For detailed information about these parameters refer to the table below Pre PCR segment PCR segment Post PCR segment Number of temperature control parameters in the pre PCR segment Number of temperature control parameters in the PCR segment Number of cycles the PCR segment will run Number of temperature control parameters in the ...

Page 75: ...F5 F2 Start Cancel More Print Store If you want to Then start running the default method press Start store the method under a user s name press Store print a record of the method parameters press Print enter temperature control parameters enter the information on the create screen and create a new method display more functions for modifying methods press More Note The More function only displays w...

Page 76: ...gure 5 1 Number Description 1 Number of pre PCR holds 2 Pre PCR temperature parameter 3 Pre PCR hold time parameter 4 Number of PCR segment temperatures 5 Number of cycles for the PCR segment 6 PCR segment temperature parameter 7 PCR segment time parameter 8 PCR segment temperature parameter 9 PCR segment time parameter 10 PCR segment temperature parameter 11 PCR segment time parameter 12 Number o...

Page 77: ...ent from your method 2 Create the first temperature parameter a Press Enter b Type in a temperature value between 4 0 C and 99 9 C 3 Create the first hold time parameter a Press Enter b Type in a hold time value between 00 00 and 98 59 minutes seconds 4 Enter information for the next pre PCR hold a Press Enter b Repeat step 2 and step 3 until you have hold time and temperature values for each of t...

Page 78: ...ues for each of the segment temperature control parameters you defined in step 1 To define the PCR parameters continued Step Action Temperature Time min sec Use For 72 C 7 00 Complete extension of all amplicons 72 C 99 59 AmpErase applications 4 C 99 59 General storage To define post PCR holds Step Action 1 Select the Holds field 2 In the Holds field type in the number of post PCR steps for your m...

Page 79: ...cally increase or decrease the value for any PCR segment parameter by a fixed amount every cycle Note This feature is particularly useful towards the end of the amplification process since the amount of PCR product available to be extended increases with the number of cycles while the amount of available enzyme remains constant To automatically change temperature control parameters Step Action 1 F...

Page 80: ...d plus sign decrease the value every cycle a minus sign displays in the current field minus sign To modify ramp rates Step Action 1 Press Modify from the Modify screen The Select Modification screen appears 2 Press Ramp The Ramp Rate Modification screen appears In this example you can modify the rate at which the instrument ramps up from 72 0 C to 94 0 C down from 94 0 C to 55 0 C or up from 55 0 ...

Page 81: ...ates continued Step Action If you want to Then press increase the ramp rate by 10 up to a maximum of 100 the Faster key decrease the ramp rate by 10 from 100 to 10 and by 5 from 10 to 5 the Slower key To insert holds Step Action 1 From the Create screen use the Circular Key Pad to select a time or temperature parameter to the right of where you want to insert a hold 2 Press More Depending on the p...

Page 82: ...rcular Key Pad to select a time or temperature parameter to the right of where you want to insert a cycle 2 Press More Depending on the parameter you select in step 1 one of three screens displays from which you can access the insert function 3 Press Insert The Insert screen appears 4 Press Cycle to insert a cycle to the left of the segment you selected in step 2 Note You can delete a cycle by ent...

Page 83: ...h pause 7 In the Cycles For field type in the length of the pause in minutes seconds 00 01 98 59 format 8 In the Beep During The Pause field press Yes or No 9 Press Accept to accept the pause information on the screen The word Pause now displays to the right of the incubation step where you programmed the pause Note You can only insert one pause in each cycle To insert a programmed pause continued...

Page 84: ...erent time After you have entered all modifications to the customized method you are creating you should store the method before running it see Naming and Storing Methods below To name and store methods Step Action 1 From the Create screen press Store 2 You can take the following action 3 From the Store screen press Method The Method Name screen appears Note The blank space after the letter Z is u...

Page 85: ...ld now display in the Method Name field 6 From the Store screen press Accept This stores the method under the name you entered To name and store methods continued Step Action Step Action a Use the Circular Key Pad to select a character in the list shown in the upper right portion of the screen b After selecting a character press Enter to place the character in the Method Name field c If you want t...

Page 86: ...ds on Inst User Size Stored or Last Used or on PC card Used Mem xxx methods xxx segments Free Mem xxx methods xxx segments The following table describes these fields 2 Select one of the methods displayed on the screen or select another method as follows Field Description units for the Size field Based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size...

Page 87: ... parameters on the Create screen involves the same tasks and uses the same key combinations as you use when creating a method The same functions for modifying methods are also available 6 From the Edit screen press Store to store the method To edit a method continued Step Action 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 55 0 94 0 2 00 10 00 55 0 0 30 72 0 0 30 72 0 5 00 4 0 94 0 0 30 F1 F3 F4 F5 F2 Hold C...

Page 88: ... or select another method as follows 3 Press Delete The Delete Confirmation screen appears If the method is protected enter a four digit PIN and press Accept when the number is correct Press Yes to delete the method Delete Method Methods on Inst exp001 User lisa Size 15 Stored 01 01 00 F1 F3 F4 F5 F2 Yes Cancel Field Description Units for the Size field Based on a calculation of the complexity and...

Page 89: ...on 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 To delete a method continued Step Action ...

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Page 91: ...mation 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 GeneAmp PCR System 2400 or 9600 may be transported to the GeneAmp PCR System 9700 without change when using the 9600 emulation mode In This Chapter The following topics are covered in this chapter Topic See page About Setting Hold Times 6 ...

Page 92: ...old Time Differences As shown in the figures below since the block reaches the target temperature before the sample the programmed hold time on the DNA Thermal Cycler and the DNA Thermal Cycler 480 must include enough time for the samples to reach the target temperature A hold time of one minute or greater is required on the DNA Thermal Cycler and the DNA Thermal Cycler 480 for samples to reach th...

Page 93: ...base the new hold time For more information see an up ramp on the change in the temperature required to reach the next target temperature Table 6 1 on page 6 3 a down ramp on the starting temperature of the ramp and the change in temperature required to reach the next temperature Table 6 2 on page 6 5 Step Action 1 Determine the change in temperature required to reach the next target temperature a...

Page 94: ...times Add the indicated times instead of subtracting them Setting Down Ramps The following table lists the process of setting the down ramp temperature 80 sec Hold Time 72 55 Temp C temp 17 round to 15 DNA Thermal Cycler 35 sec Hold Time 72 55 Temp C GeneAmp PCR System 9700 Step Action 1 Determine the change in temperature required to reach the next target temperature and round this value off to t...

Page 95: ...r the DNA 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 Table 6 2 Converting down ramp hold times A Temp C Starting temperature of ramp C 35 55 56 75 76 96 10 39 ...

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Page 97: ...er There are no components inside the GeneAmp PCR System 9700 that you can safely service yourself If you suspect a problem contact an Applied Biosystems Technical Support Representative In This Chapter The following topics are covered in this chapter CAUTION Topic See page Changing the External Fuses 7 2 Changing Fuses for Single Line Operation 7 3 Changing Fuses for Double Line Operation 7 4 ...

Page 98: ...instrument All instruments have factory installed fuses However if you should ever need to change a fuse or if you need to convert from the factory configured single line service to double line service follow the instructions that follow in this chapter Power Entry Module Diagram The Power Entry Module is located at the rear of the left side of the instrument CAUTION GR0961 Jumper clip Fuse compar...

Page 99: ...power supply is operating To avoid electrical shock disconnect the power supply to the instrument unplug the power cord and wait at least 1 minute before working on the instrument The fuse is located in the Power Entry Module 2 Insert a small flat tip screwdriver into the slot in the upper portion of the power entry module and open the door 3 Pull the fuse compartment out There is one fuse in the ...

Page 100: ...s operating To avoid electrical shock disconnect the power supply to the instrument unplug the power cord and wait at least 1 minute before working on the instrument The fuses are located in the Power Entry Module 2 Insert a small flat tip screwdriver into the slot in the upper portion of the power entry module and open the door 3 Pull the fuse compartment out There are two fuses in the fuse compa...

Page 101: ... 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 8 2 Display Screen Error Messages 8 3 Troubleshooting Information 8 6 ...

Page 102: ...l restart If the power fails while executing a hold or approaching a hold then that hold temperature will restart from the beginning Note If the power failure lasts longer than 18 hours the Resume will not occur Do the following in a power failure Step Action 1 Restart or continue the PCR experiment The instrument determines what temperature was being approached or was holding Upon resumption of p...

Page 103: ...ity hold as the last segment in a method This message occurs when you try to enter an infinity hold segment in the middle of a method Assign finite time segments to holds within a method Can t allocate timer System error Call Technical Support Delete your methods first User tried to delete a user name that has methods stored under it Delete or transfer the associated methods before deleting a user...

Page 104: ...ore than six hold or cycle parameters to a method Method battery RAM initialized Stored methods have been reset due to hardware or software failure Not all methods may be lost Check method directory Call Technical Support Method requires at least one segment You deleted all temperature control parameters in a method A method must have at least one time and temperature parameter Review and correct ...

Page 105: ...f range Tm out of range Check input value and retry Call Technical Support User name already defined You entered a user name that already exists Do not duplicate user names WARNING Block version unknown Some data in the block is unrecognized Instrument operation will not be effected Upgrade firmware Watchdog timeout Software failure Call Technical Support Write to block failed Information written ...

Page 106: ...w Peltier failure Run Rate Test diagnostic Call Applied Biosystems Technical Support Instrument can t reach high or low temperature range Ambient temperature is too warm Peltier failure Run Rate Test diagnostic Run Cycle Test diagnostic Call Technical Support Instrument making too much noise Fan failure Check for sidevent obstructions No beep Run time beeper disabled Beeper failure Check Run Time ...

Page 107: ...al specifications for the GeneAmp PCR System 9700 system including the control panel sample temperature information and printer specifications In This Appendix The following topics are covered in this appendix Topic See page System Specifications A 2 Control Panel Specifications A 3 Sample Temperature Information A 3 Printer Specifications A 3 ...

Page 108: ...electrical operating range for the instrument in various parts of the world Select appropriate fuse configuration based on the voltage used In Japan the unit must have a dedicated 220 volt outlet The unit will not operate properly with a 100 volt outlet Note The Volt Amp number for this instrument is 725Volt Amps Height 26 cm 10 in Width 28 cm 11 in Depth 41 cm 16 in Base Module 8 6 kg 19 lbs 96 W...

Page 109: ...lowing table lists sample temperature information Note Sample temperatures are displayed in degrees Celsius to the nearest 0 1 C Printer Specifications Serial Interface Board Specifications The instrument can use any printer with a serial RS 232C interface board with the following parameters Cable Part Number Connect the printer to the Instrument port with printer cable part number N805 1326 Sampl...

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Page 111: ...n about the methods that are supplied with the GeneAmp PCR System 9700 In This Appendix The following topics are covered in this appendix Topic See page About the Methods B 2 AmpliCycle Sequencing B 2 AmpliTaq Gold B 2 BigDye B 3 General PCR B 3 LMS2 B 4 Time Release PCR B 4 Touchdown PCR B 5 XL PCR B 5 ...

Page 112: ...rs from femtomole amounts of template This cycle sequencing process and the benefits of AmpliTaq DNA Polymerase CS are described in the product insert for the AmpliCycle Sequencing Kit P N N808 0175 AmpliTaq Gold The AmpliTaq Gold protocol specifies a 5 minute pre PCR heat step required for the activation of AmpliTaq Goldâ DNA Polymerase This additional step provides seamless hot start PCR and rep...

Page 113: ... It consists of 25 cycle three temperature cycle sequencing followed by an infinite hold at 4 C The pre coded conditions in the BigDyeä method are optimized for AmpliTaq DNA Polymerase FS and the cycle sequencing reagents supplied with the BigDye terminator kits This process is further described in the ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction Kits Protocol P N 4303237 General PC...

Page 114: ...ection and data analysis Time Release PCR The Time Release PCR method is designed for use with AmpliTaq Gold DNA Polymerase The enzyme is activated more slowly than with the AmpliTaq Gold method Here the pre PCR hold is only 1 minute and the number of cycles is increased to 40 1 Weissenbach J et al 1992 A second generation linkage map of the human genome Nature 359 794 801 2 Gyapay G et al 1994 Gé...

Page 115: ...seconds 68 C for 10 minutes and invokes a 15 second AutoX automatic segment extension for the anneal extend step in the last 12 cycles By providing longer templates XL PCR complements technologies for rapid long range PCR More complete genes can be amplified in one reaction from known expressed sequences thus more introns can be crossed You can use XL PCR for the amplification of the control targe...

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Page 117: ...tion you can download documents in PDF format from the Applied Biosystems web site Please see the section To Obtain Technical Documents following the telephone information below To Contact Technical Support by E Mail You can contact Applied Biosystems Technical Support by e mail for help in the following product areas Product Product Area E mail address Genetic Analysis DNA Sequencing galab applie...

Page 118: ... Custom and Synthesis Pioneer Peptide Synthesizers Proteomics Solution 1 PS1 Systems ICAT Reagent FMATä 8100 HTS Systems Marinerä ESI TOF Mass Spectrometry Workstations Voyagerä MALDI TOF Biospectrometry Workstations CytoFluor 4000 Fluorescence Plate Reader tsupport appliedbiosystems com LC MS Applied Biosystems MDS Sciex support sciex com Chemiluminescence Tropix tropix appliedbiosystems com Prod...

Page 119: ...ed Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 press 2 then press 4a 1 650 638 5981 ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 press 2 then press 6a 1 650 638 5981 Peptide Synthesis 433 and 43x Systems 1 800 831 6844 press 3 then press 1a 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 press 3 then press 2a 1 650 638 5981 Sequen...

Page 120: ...then press 6b 1 508 383 7855 Chemiluminescence Tropix 1 800 542 2369 U S only or 1 781 271 0045c 1 781 275 8581 LC MS Applied Biosystems MDS Sciex 1 800 952 4716 1 508 383 7899 Product Product Area Telephone Fax Region Telephone Fax Eastern Asia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 or 86 800 8100497 86 10 64106617 Hong Kong 852 2756 6...

Page 121: ...ca 27 11 478 0411 27 11 478 0349 Africa French speaking Paris France 33 1 69 59 85 11 33 1 69 59 85 00 India New Delhi 91 11 653 3743 91 11 653 3744 91 11 653 3138 Poland Lithuania Latvia and Estonia Warszawa 48 22 866 40 10 48 22 866 40 20 For all other EMT countries not listed Central and southeast Europe CIS Middle East and West Asia 44 1925 282481 44 1925 282509 Japan Japan Hacchobori Chuo Ku ...

Page 122: ...region for the product area of interest 4 Follow the instructions under the Frequently Asked Questions section 1 to display a list of FAQs for your area of interest To search for solutions to problems using the Solution Database Step Action 1 Go to http www appliedbiosystems com 2 Click SERVICES SUPPORT at the top of the page then click Frequently Asked Questions 3 Follow the instructions under th...

Page 123: ... on Demand 3 In the search form enter and select search criteria then click Search at the bottom of the page 4 In the results screen do any of the following Click the pdf icon to view a PDF version of the document Right click the pdf icon then select Save Target As to download a copy of the PDF file Select the Fax check box then click Deliver Selected Documents Now to have the document faxed to yo...

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Page 125: ...eems necessary to correct covered defects or failures of which Applied Biosystems is notified prior to expiration of the Warranty Period All repairs and replacements under this Warranty shall be performed by Applied Biosystems s service engineers or designees No agent employee or representative of Applied Biosystems has any authority to bind Applied Biosystems to any affirmation representation or ...

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Page 127: ...10 customer support See technical support C 1 cycles counting of 4 7 inserting 5 14 cycling modifying 5 11 to 5 17 AutoX function using 5 11 to 5 12 cycles inserting 5 14 deleting holds 5 14 holds inserting 5 13 ramp rates modifying 5 12 to 5 13 D data bit serial board specifications 3 11 3 27 date last used sorting methods by 4 5 setting 3 9 deleting methods 5 18 to 5 21 user name 5 5 diagnostic ...

Page 128: ...instrument 3 7 unpacking 3 2 General PCR 4 2 B 2 General PCR about supplied method B 3 grounding 1 11 H Hard soft key function of 3 14 hazards and warnings 1 3 to 1 8 1 9 to 1 11 burns danger of 1 10 electrical shock hazard 1 10 fire hazard 1 11 instrument warnings 1 9 heated cover screen 4 7 heating of samples 5 8 history of run reviewing history file records 4 11 history formats 4 10 procedure 4...

Page 129: ...me 2 3 temperature control 5 11 temperature parameters 2 3 See Also custom parameters setting parity bit 3 11 3 27 part numbers for ordering accessories 3 2 fuse part number 3 5 Pause Time Out setting 3 10 pauses programmed editing 5 16 inserting 5 14 PCMCIA card using to copy methods 3 25 to 3 26 using to upgrade firmware 3 23 3 24 PCR holds defining 5 9 to 5 10 PCR samples running methods runnin...

Page 130: ... 2 Time Release PCR 4 2 B 2 Time Release PCR about supplied method B 4 time setting 3 9 TM calculator how to use 3 18 Tmp field using to define temperature control parameters 5 9 TmpVer soft key function of 3 14 ToCard softkey function of 3 26 ToInst softkey function of 3 26 Touchdown PCR 4 2 B 2 about supplied method B 5 training obtaining information C 7 troubleshooting 8 1 to 8 6 display screen...

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Page 132: ...0 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 or to the Technical Support and Training appendix in this document www appliedbiosystems com Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of ...

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