Applied Biosystems 2720 Thermal Cycler User Guide (PN 4359453
Contents
1. 4 1 Adding Changing or Deleting a User Name 4 2 Creating a Method 4 6 Changing a Method Using Advanced Features 4 9 Handling Methods 4 18 5 Utilities Overview 5 1 Configuring the Instrument 5 2 Upgrading System Firmware 5 4 Connecting to a Printer 5 5 Calculating the Melting Temperature 5 6 Running Hardware Diagnostics 5 7 Running the Calibratio2. xx Safety and Electromagnetic Compatibility EMC Standards xxi 1 System Overview Overview 1 1 Introducing the Applied Biosystems 2720 Thermal Cycler 1 2 About the Control Panel 1 4 Overview of Functions 1 5 Introducing an Important Screen 1 6 2 Getting Started Overview 2 1 Powering On 2 2 Adding Yourself as a User 2 3 Creating a Method
3. A 1 System Specifications A 2 Control Panel Specifications A 2 Sample Temperature Information A 3 Printer Specifications A 3 B Supplied Methods Overview B 1 About the Methods B 2 C Screen Flowcharts Overview C 1 Run C 2 Stop or End of Run C 3 Create Edit
4. C 4 User C 5 Utilities C 6 Diagnostics C 7 Upgrade C 8 D Instrument Warranty Information Overview D 1 Computer Configuration D 2 Limited Product Warranty D 2 Damages Claims and Returns D 4 Index vi DRAFT October 22 2010 3 44 pm Preface fm vii Preface How to Use This Guide Purpose of This Guide The Applied Biosystems 2720 Thermal Cycler User Manual describes how to use the Applied Biosystems 2720 Thermal Cycler The user manual provide
5. viii How to Obtain Support viii Safety and EMC Compliance Information Safety Conventions Used in This Document x Symbols on Instruments xi Safety Labels on Instruments xii Instrument Warnings Diagram xiv General Instrument Safety xv Chemical Safety xv Chemical Waste Safety xvii Electrical Safety xviii Laboratory Environmental Requirements xx Physical Hazard Safety
6. Interchangeable sample blocks with 60 96 or dual 384 wells Networking capabilities High instrument diagnostics capabilities Variable ramp rates and cycling speeds PCMCIA slot for software upgrade and Methods Transportability card 1 4 System Overview About the Control Panel Overview The control panel for the 2720 Thermal Cycler consists of a display screen and keys including function keys F1 F5 numeric keys arrow keys and the Enter CE and Stop keys as shown in the figure below Display The display screen is a window that you use for communicating with the instrument s software F1 to F5 Keys Use the function keys F1 to F5 to activate the button on the screen above the key for example F1 for Run The display is not a touch screen Throughout this manual you will find instructions to press F1 Run or press F2 Create The function keys permit you to navigate from screen to screen and perform other actions Selecting a Field Most screens have a highlighter that you use to select a field To move the highlighter use the arrow keys or the Enter key Entering Numbers Use the numeric keys 0 9 to enter numeric values then press Enter or an arrow key When you type temperatures and times minutes seconds the system takes care of the decimal point and colon respectively If necessary you can use the CE key to clear a field and then reenter values 08 00 AM 09 25 00
7. Access our Web site a Sensor error in Cycle xx Setpt xx Repxx Cover sensor failure Heated cover sensor failure Fatal error Access our Web site a Setpt error in Cycle xx Setpt xx Repxx Could not reach xx x in hh mm ss This setpoint error is only logged for setpoints above 15 C The limit is 5 times the normal ramping time Fatal error Access our Web site a Program pause in Cycle xx Setpt xx Rep xxx Method paused at xx C for hh mm ss A programmed pause was encountered Report Manual pause in Cycle xx Setpt xx Rep xxx Method paused at xx C for hh mm ss You paused the run Report a http www appliedbiosystems com support contact Runs 3 13 When a Run Completes End of Run Screen When a run ends the End of Run screen appears However if your method has an indefinite hold of 4 C for example you must first press the Stop key to display the screen shown below If you created a new method but have not stored it when F5 Exit is pressed the Method Not Stored screen displays to give you the opportunity to save the method before returning to the Main Menu Method Not Stored Screen If you attempt to exit the End of Run screen before storing a new method the Method Not Stored screen appears If you want to store the method press F2 Store For more information about naming and storing a method see Creating a Method on page 4 6 11 30 AM 25 1 C Method General PCR Run completed
8. ENTER STOP F1 F2 F3 F4 F5 1 2 3 4 5 6 7 8 9 0 CE F1 F3 F4 F5 F2 Utilities 5 9 Running the Calibration Verification Test Why Use This Test Use this test to verify the temperature calibration of your 2720 Thermal Cycler Equipment Required This test requires the 0 2 mL Temperature Verification System P N 4317939 for 96 well thermal cyclers For more information on performing the test refer to the instructions included with your Temperature Verification System Follow the procedure for the GeneAmp PCR System 9700 Running the Temperature Non Uniformity Test Why Use This Test Use this test to verify the temperature non uniformity of the sample block in the 2720 Thermal Cycler Equipment Required This test requires the 0 2 mL Temperature Verification System P N 4317939 for 96 well thermal cyclers For more information on performing the test refer to the instructions included with your Temperature Verification System Follow the procedure for the GeneAmp PCR System 9700 5 10 Utilities Running System Performance Diagnostics Overview After you have configured the 2720 Thermal Cycler conduct the system performance tests to verify the integrity of the cooling and heating system There are two system performance tests Rate Test Cycle Test IMPORTANT Before you begin these tests make sure that you place an empty 96 well plate with full plate cover on the sample block
9. More Delete Insert Edit 0 30 Pause To automatically increase or decrease temperature control parameters Step Action 1 Use the arrow keys from the Create Edit screen to select a time or temperature parameter in the PCR segment 2 Press F4 More The Modify screen appears 3 Press F1 Modify The Select Modification screen appears 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 Modify More Delete Insert Select Modification F1 F3 F4 F5 F2 AutoX Cancel Increments or decrements time or temperature at the completion of each cycle AutoX Methods and Users 4 17 4 Press F1 AutoX The AutoX screen appears Note If you have inserted a programmed pause the AutoX screen displays the pause but you cannot modify it from the AutoX screen 5 Highlight the PCR time or temperature parameter that you want modified when you run your method Note From the AutoX screen you cannot modify the number of parameters in each segment or the number of cycles 6 Use the numeric keypad to change numeric values Press F2 or F3 to change the plus or minus signs The selected sign displays in the current field After you press Enter or an arrow key an asterisk appears for parameters that have been modified 7 Press F1 Accept to accept all entries on the AutoX screen and return to the Modify screen 8 Pr
10. ve added a hold another time and temperature segment to the graph 4 Press F2 Store to save the method The Store Method on Instrument screen appears The system has given the method a default name of exp000 We will use a different name 5 Press F3 Method The Method Name screen appears 6 Press the CE key to clear the field Then spell out test01 by highlighting each letter and pressing Enter after each one 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 Start Cancel More Print Store Store Method on Instrument F1 F3 F4 F5 F2 Accept Cancel Method User Method exp000 Free Mem 122 methods 946 segments User adrian Use ENTER key to select a character Method Name exp000 F1 F3 F4 F5 F2 Accept Cancel Backsp abcdefghi jklmnopqrj stuvwxyz 2 6 Getting Started 7 Press F1 Accept The Store Method on Instrument screen appears again with test01 as the method name On the 2720 Thermal Cycler a method has a method name and it is associated with a particular user 8 Press F1 Accept The system saves your method and returns to the Main Menu To create a method continued Step Action Getting Started 2 7 Editing Your Method Procedure To edit the method Step Action 1 From the Main Menu press F2 Edit The Stored Methods screen appears You have on
11. 02 22 00 02 10 00 02 02 00 4 20 Methods and Users Viewing Method Parameters 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 view the parameters of a method before running it Step Action 1 Press F2 View from the Stored Methods screen The View Method screen appears The screen shows all the parameters of the method you selected 2 After reviewing PCR and post PCR parameters of a stored method you can Press F1 Start to start the method Press F5 Return and return to the Stored Methods screen 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 sort methods Step Action 1 Press F4 Sort from the Stored Methods screen The Sort Methods screen appears Sort Methods By Method name Date last used Date stored Method size F1 F3 F4 F5 F2 Accept Cancel Methods and Users 4 21 Searching for Methods You can find any method that has been stored under a user name 2 Use the up and down arrow keys to select the type of sort The following table describes the sort methods 3 Press F1 Accept to accept a selection This returns you to the Stored Methods screen where the displayed methods are sorted according
12. 12 13 02 22 00 02 10 00 02 02 00 Select Method Options Enter a value from 5 to 100 L Reaction Volume 50 L F1 F3 F4 F5 F2 Start Cancel Current temperature 65 C The run will begin when the heated cover reaches 103 C Please wait Cover is heating F1 F3 F4 F5 F2 Cancel 3 8 Runs 7 Wait for the heated cover to reach 103 C The Run Time screen displays and the method you selected starts running 8 Optional To find out when the run will end press F4 Info The Method Information screen appears When you are through viewing this screen press F4 Return to redisplay the Run Time screen To start a run continued Step Action 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 02 32 PM Information 55 2 C User lisa Run started at 01 32 30 PM 03 01 00 Run will end at 06 35 30 PM 03 01 00 Reaction vol 50 L Method General PCR F1 F3 F4 F5 F2 Return Runs 3 9 Pausing or Stopping a Run Overview This section describes how you can pause a run or stop it completely Pausing a Run During a run the Run Time screen is displayed From this screen you can pause a run for a prespecified length of time and then resume it For example you might pause a run in order to add a reagent Note Do not touch the sample block or the bottom of the heated cover dur
13. Cycle Time STD lt 1 0 sec Maintenance 6 1 Maintenance 6 Overview About This Chapter This chapter provides procedures for maintaining your Applied Biosystems 2720 Thermal Cycler Do not remove the instrument cover There are no components inside the 2720 Thermal Cycler that you can safely service yourself If you suspect a problem refer to our Web site http www appliedbiosystems com 2720 In This Chapter This chapter contains the following topics Topic See Page Cleaning the Instrument 6 2 Replacing Fuses 6 4 6 6 2 Maintenance Cleaning the Instrument Preparation To clean the sample wells raise the lid The cleaning position is shown below Cleaning the Sample Wells If you use any cleaning or decontamination method except those recommended in the manual you risk damaging the equipment Clean the sample wells once a month or as needed During instrument operation the temperature of the heated cover can be as high as 108 C and the temperature of the sample block can be as high as 100 C Before performing the procedure keep hands away until the heated cover and sample block reach room temperature GR1988 Heated platen Heated cover Sample wells To clean the sample wells Step Action 1 If a method is running press the Stop key twice 2 Turn off the instrument 3 Wait 1 minute for the block to cool 4 Lift the lever and open the hinged heated cover 5 Remove the sam
14. Returns Do not return any material without prior notification and authorization If for any reason it becomes necessary to return material to Applied Biosystems contact Applied Biosystems Technical Support or your nearest Applied Biosystems subsidiary or distributor for a return authorization RA number and forwarding address Place the RA number in a prominent location on the outside of the shipping container and return the material to the address designated by the Applied Biosystems representative Index 1 Index A AmpliTaq Gold about supplied method B 2 Applied Biosystems contacting viii customer feedback on documentation viii Information Development department viii Technical Support viii AutoX function 4 16 to 4 17 B baud rate 5 3 BigDye Terminator about supplied method B 3 biohazardous waste handling xvii bold text when to use vii C calibration verification test 5 9 CAUTION description x CE key 1 4 chemical safety xv xvi chemical waste safety xvii claims processing D 4 cleaning instrument 6 2 to 6 3 compressed gases safety See also pressurized fluids safety xx computer configuration requirement D 2 technical support for altered configuration D 2 configuring instrument 5 2 to 5 3 control panel 1 4 conventions bold text vii for describing menu commands vii IMPORTANTS vii in this guide vii italic text vii Notes vii safety x user attention words vii create edit flowchart of screens C 4 scre
15. Tm of P1 Tm of P2 Press ENTER to calculate Tm s Tm Calculator Go to Utilities 1 Go to Configuration 1 Method is gone unless it was locked See Diagnostics chart Methods exp000 exp0001 exp001a exp002 User faye faye faye faye F1 F3 F4 F5 F2 Delete Cancel Sort User View Size 11 6 9 8 LastUsed 11 16 99 11 16 99 11 16 99 11 16 99 Stored Methods Press Yes to delete the method Delete Method Methods on Inst exp001 User lisa Size 15 Stored 09 01 96 F1 F3 F4 F5 F2 Yes Cancel Delete Method Configuration 1 F1 F3 F4 F5 F2 Accept Cancel More 24Hr PM Instrument Configuration Time 11 30 AM Date 03 01 00 M D Y Run Time Printer Off Configuration 2 Instrument Configuration Pause Time Out 10 00 00 01 99 59 Idle State Setpoint 25 0 C 4 0 99 9 Baud Rate 9600 F1 F3 F4 F5 F2 Accept Cancel More Main Menu 08 00 AM 09 25 00 25 0 C GeneAmp PCR System 2700 User adrian F1 F3 F4 F5 F2 Run User Util Edit Create Version Utilities 2 Utilities Delete Delete a Method Hist Display history of last run F1 F3 F4 F5 F2 Delete Exit More Hist Applied Biosystems Thermal Cycler Screen Flowcharts C 7 Diagnostics Diagnostics Hard Hardware Diagnostics System System Performance Tests TmpVer Temperature Verification Upgrad Firmware Upgrade F1 F3 F4 F5 F2 Hard Exit Upgrad TmpVer Sy
16. You must create a separate a Sample Entry Spreadsheet for each 96 well plate The lamp is extremely hot Do not touch the lamp until it has cooled to room temperature CHEMICAL HAZARD Formamide Exposure causes eye skin and respiratory tract irritation It is a possible developmental and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves ELECTRICAL HAZARD Failure to ground the instrument properly can lead to an electrical shock Ground the instrument according to the provided instructions DRAFT October 22 2010 3 44 pm Safety_HW fm xi Symbols on Instruments Electrical Symbols on Instruments The following table describes the electrical symbols that may be displayed on Applied Biosystems instruments Safety Symbols The following table describes the safety symbols that may be displayed 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 xii These safety symbols may also appear next to DANGERS WARNINGS and CAUTIONS that occur in the text of this and other product support documents Symbol Description Indicates the On position of the main power switch Indicates the Off position of the main power switch Indicates the On Off position of a push push main power switch Indicates a terminal that may be connec
17. chemical waste xvii compressed gases xx conventions x electrical xviii guidelines xvi xvii instrument operation xv moving and lifting instrument xv moving parts xx moving lifting xv physical hazard xx standards xxi safety labels on instruments xii safety standards xxi safety symbols on instruments xi sample block cleaning 6 2 to 6 3 sample tubes 3 2 to 3 4 samples loading 3 5 to 3 6 removing 3 6 specifications A 2 to A 3 standards EMC xxi safety xxi starting 2 1 to 2 11 stop key 1 4 stop flowchart of screens C 3 symbols safety xi system 2700 Index 3 functions 1 5 overview 1 2 to 1 3 2 10 to 2 11 T Technical Support contacting viii technical support for computers with altered configuration D 2 temperature control 4 16 to 4 17 idle state setpoint 5 3 melting calculating 5 6 specifications A 3 verification test 5 9 text conventions vii Time Release PCR about supplied method B 3 time configuring 5 3 Tm calculator 5 6 Touchdown PCR about supplied method B 4 training information on viii troubleshooting 7 1 to 7 6 U upgrade flowshart of screens C 8 user attention words described vii user name adding 2 3 to 2 4 4 2 to 4 4 changing 4 4 to 4 5 deleting 4 5 flowchart of screens C 5 utilities flowchart of screens C 6 procedures 5 1 to 5 12 W WARNING description x warranty damages claims returns D 4 for computers with altered configuration D 2 limitations D 3 war
18. murray nayana ngui Use ENTER key to select a character User Name F1 F3 F4 F5 F2 Accept Cancel Backsp abcdefghi jklmnopqrj stuvwxyz User Name adrian Press PIN to create a Then you set protection to Locked to prevent methods from being overwritten or deleted PIN number None Protection Unlocked F1 F3 F4 F5 F2 Accept Cancel PIN Name 2 4 Getting Started 4 Press F5 Cancel You can learn about security later The Select User Name screen appears 5 With your name highlighted press F1 Accept to return to the Main Menu To add yourself as a user continued Step Action Select User Name F1 F3 F4 F5 F2 Accept Cancel Delete Edit New lt lt ab gt gt adrian anna dave doug faye jenife mamood mike murray nayana ngui Getting Started 2 5 Creating a Method Procedure To create a method Step Action 1 From the Main Menu press F2 Create The Create Edit screen appears with a default method displayed 2 Use the arrow keys to move the highlighter to a temperature or time on the graph and change the parameter For example move the highlighter to the 5 00 time at the left of the screen in the pre PCR portion Press 5 3 0 then press Enter for 5 30 3 Make a change to the top line For example use the arrow keys to move the highlighter to the 1 in the upper left corner of the screen Press 2 then Enter Notice that you
19. s already highlighted selected 2 Press F1 Start The Select Method Options screen appears 3 Change the reaction volume to 40 then press F1 Start The Run Time screen appears Methods test01 User adrian F1 F3 F4 F5 F2 Start Cancel Sort User View Size 11 LastUsed 01 04 00 Select Method Options Enter a value from 5 to 100 L Reaction Volume 50 L F1 F3 F4 F5 F2 Start Cancel Sample temperature increments Flashes to warn you 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 Getting Started 2 9 4 Press the Stop key The Confirm Stop screen appears 5 Press the Stop key again to abort the run The End of Run screen appears 6 Press F5 Exit to return to the Main Menu To start then stop a run continued Step Action Sample 50 1 Confirm Stop HOT Press STOP to abort Press Resume to continue F1 F3 F4 F5 F2 Resume 11 30 AM 25 1 C Method test01 Run aborted at 11 30 05 AM 01 04 00 Length of run is 01 34 25 End of Run F1 F3 F4 F5 F2 Hist Exit 2 10 Getting Started More Features Overview Now you know the basics of operating the 2720 Thermal Cycler The system provides additional features Some things you might try are discussed below Navigating from the Main Menu Explore paths from the Main Menu to find out what
20. 0 0 30 0 0 0 00 0 0 0 00 F1 F3 F4 F5 F2 Accept Cancel AutoX 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 Modify More Delete Insert Modify 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 Cancel Pause Cycle Insert Go to Create Edit The Modify key is present only when you highlight a PCR temperature or time The Insert and Delete keys are present only when you highlight any temperature or time Deletes highlighted segment Store Method on Instrument User Method exp002 F1 F3 F4 F5 F2 Accept Cancel Method User Free Mem 122 methods 946 segments april Store Method on Instrument Go to Select User Name Use ENTER key to select a character Method Name exp001 F1 F3 F4 F5 F2 Accept Cancel Backsp abcdefghi jklmnopqrj stuvwxyz Method Name Inserts a hold or cycle to the left of the highlighted time or temperature Inserts a pause Then you can edit the pause or go to Create Edit You can highlight parameters and type in new values here Select Modification Select Modification F1 F3 F4 F5 F2 AutoX Cancel Increments or decrements time or temperature at the completion of each cycle AutoX Define Programmed Pause Define
21. 2 5 Editing Your Method 2 7 Starting and Stopping a Run 2 8 More Features 2 10 iv 3 Runs Overview 3 1 Using Disposables 3 2 Loading Samples 3 5 Starting a Run 3 7 Pausing or Stopping a Run 3 9 Reviewing the History of a Run 3 11 When a Run Completes 3 13 4 Methods and Users Overview
22. 72 0 7 00 4 0 F1 F3 F4 F5 F2 Hold Cancel Pause Cycle Methods and Users 4 11 Deleting a Hold There are two ways to delete a hold You can decrement the value of the Hld Tmp or Holds fields on the Create Edit screen then press Enter This deletes a hold at the far right of the pre PCR PCR or post PCR segment separated by dashed lines respectively You can use the procedure described below to delete a hold you highlight 4 Press F1 Hold The Insert Delete More screen appears showing the hold you added Note The Modify function F1 also displays if the inserted hold was in the PCR segment 5 Change the temperature and time of the new hold as necessary 6 Press F4 More to return to the Create Edit screen To insert a hold continued Step Action 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 More Delete Insert 4 0 0 30 To delete a hold Step Action 1 From the Create Edit screen use the arrow keys to highlight a time or temperature of a hold segment you want to delete 2 Press F4 More The Insert Delete More screen appears Note The Modify function F1 also displays if the highlighted parameter was in the PCR segment 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 More Delete Insert 4 12 Methods a
23. C 99 59 General storage Methods and Users 4 9 Changing a Method Using Advanced Features Introduction The previous section told you how to create and store a method If you want to change a method or make a more complex method the features described in this section will help Editing a Method To edit an existing method Step Action 1 From the Main Menu press F3 Edit The Stored Methods screen appears 2 Highlight the method you want to change then press F1 Edit The Create Edit screen appears This screen is the same one that can be accessed by pressing F2 Create from the Main Menu Once you have reached this screen you can perform the same functions regardless of how you accessed it From this screen you can Methods appl01 User adrian F1 F3 F4 F5 F2 Edit Cancel Sort User View Size 11 LastUsed 03 04 00 exp000 exp001 exp002 adrian adrian adrian 10 12 13 02 22 00 02 10 00 02 02 00 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 5 00 0 30 55 0 0 30 72 0 0 30 72 0 7 00 4 0 F1 F3 F4 F5 F2 Start Cancel More Print Store Action See Topic Page Change parameters displayed on this screen Creating a Method 4 6 Use advanced features Inserting a Hold Deleting a Hold Inserting a Cycle Inserting a Programmed Pause Editing a Programmed Pause Deleting a Programmed Pause Auto Incrementing Decrementing Temperature Control Parameter
24. Connecting to a Printer on page 5 5 Pause Time Out Use the numeric keys to enter the minutes seconds in the range shown on the configuration screen This field sets the length of time the instrument pauses when you press F1 Pause or the Stop key from the Run Time screen See Pausing or Stopping a Run on page 3 9 Idle State Setpoint Use the numeric keys to type a temperature in the range shown on the configuration screen This value is the temperature at which the instrument will remain when powered up but idle IMPORTANT After a run is completed or terminated there is approximately a 30 second delay before the instrument attains the specified idle state temperature This allows you to stop one method and start another before the instrument temperature changes Baud Rate Use the function keys Up and Down to choose a baud rate Values are 38400 19200 9600 4800 2400 1200 and 600 This value is the rate at which the instrument transmits data through the printer port and serial port Item Value Baud Rate 9600 Parity NONE Data Bits 8 Stop Bits 1 5 4 Utilities Upgrading System Firmware About the Upgrade When a new version of system firmware becomes available you can download it from our Web site http www appliedbiosystems com 2720 Instructions for performing the upgrade will also be posted on the Web site In order to perform the upgrade you will need to connect a PC communication cable P N
25. Cycler About the Instrument The Applied Biosystems 2720 Thermal Cycler is an automated instrument specifically designed for the amplification of nucleic acids using the GeneAmp Polymerase Chain Reaction PCR process The instrument has an integrated 96 well sample block which houses an internal Peltier heating cooling unit The sample block is made of aluminum to provide optimal thermal transfer rate Platinum sensors provide Wide temperature range 4 C to 99 9 C Accuracy 0 25 C from 35 C to 99 9 C Long term stability and high reliability The sample block accommodates several different types of MicroAmp disposable tubes and plates which must be used in order to create a sealed chamber The 2720 Thermal Cycler has an easy to use intuitive user interface which is described in About the Control Panel on page 1 4 GR1988 Sample block Control panel Power on off RS485 port System Overview 1 3 Comparing the 2720 Thermal Cycler to Previous Instruments The 2720 Thermal Cycler can be compared to the GeneAmp PCR System 9700 as shown below 2720 Thermal Cycler System 9700 Almost the same user interface as previous instruments Integrated sample block Uses same disposables as 96 well sample block on system 9700 Small footprint Instruments can be packed side by side on a bench because the air flows out the back rather than the sides
26. Description Recommended Action Can only enter an infinity hold at end A method can only have a Hold segment with an infinity 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 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 name Enter a name or CANCEL You did not enter at least one character on the User Name screen before pressing the Accept key Enter the user name to which the desired method is assigned Enter oligo sequence Incomplete TmCalc data Enter a value in the P1 and P2 fields of the TmCalc Enter user and method names or CANCEL You did not enter a user name and a method name before storing a method Specify the method name and choose a user to store a method Field is full You tried to enter more data in a field than the field size allows Reenter data within the specifications of the field Infinity hold not allowed in cycle A method can have an infinity hold segment as the last segment in the method This message occurs when you tried to enter an infinity time in a cycle segment Use finite values for cycle segments within the method Invalid password pin You entered an incorrect PIN Enter the correct PIN List of user names is full The ma
27. N805 1327 to the RS485 port on the side of the 2720 Thermal Cycler shown below to a serial port on a Microsoft Windows based computer that has Internet access GR1989 RS485 port Utilities 5 5 Connecting to a Printer Introduction If you elect to connect an optional printer to your 2720 Thermal Cycler you can print out a hard copy of the time and temperature parameters for PCR methods you create Specifications You can connect the 2720 Thermal Cycler to any printer with a serial RS 232C interface board and the following specifications Cable Connections Connect one end of your Applied Biosystems N805 1326 printer cable to the RS 485 serial port on the side panel of the 2720 Thermal Cycler and connect the other end to the serial adapter card port on the rear panel of the printer Installing a Printer See your printer manual for instructions on how to connect the printer cable to your printer and complete any other necessary installation steps After you have connected the printer cable and installed the printer you must configure the instrument for the printer See Configuring the Instrument on page 5 2 Baud Rate 9600 Parity NONE Data Bits 8 Stop Bits 1 5 6 Utilities Calculating the Melting Temperature Procedure Use the Tm Calculator to determine the denaturation temperature of a primer set of known sequence To calculate the melting temperature Step Action 1 Press F4 Util from th
28. THIS LIMITED WARRANTY STATEMENT AND ANY SUCH MODIFICATION AFFIRMATION REPRESENTATION OR WARRANTY MADE BY ANY AGENT EMPLOYEE OR REPRESENTATIVE OF APPLIED BIOSYSTEMS WILL NOT BE BINDING ON APPLIED BIOSYSTEMS UNLESS IN A WRITING SIGNED BY AN EXECUTIVE OFFICER OF APPLIED BIOSYSTEMS D 4 Instrument Warranty Information THIS WARRANTY IS LIMITED TO THE BUYER OF THE PRODUCT FROM APPLIED BIOSYSTEMS AND IS NOT TRANSFERABLE Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties of liability such as liability for gross negligence or willful misconduct or of remedies or damages as or to the extent set forth above In such countries and jurisdictions the limitation or exclusion of warranties liability remedies or damages set forth above shall apply to the fullest extent permitted by law and shall not apply to the extent prohibited by law 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 Claims After a damage inspection report is received by Applied Biosystems Applied Biosystems will process the claim unless other instructions are provided
29. a Method To print a method Step Action 1 From the Create Edit screen press F3 Print This prints a copy of the parameters for the method displayed on the screen To delete a method Step Action 1 From the Main Menu press F4 Util The Utilities 1 screen appears 2 Press F4 More The Utilities 2 screen appears 3 Press F1 Delete The Stored Methods screen appears Utilities Diag Instrument diagnostics TmCalc Calculates melting temp Config Instrument configuration F1 F3 F4 F5 F2 Diag Exit More Config TmCalc Utilities Delete Delete a Method Hist Display history of last run F1 F3 F4 F5 F2 Delete Exit More Hist Methods appl01 User adrian F1 F3 F4 F5 F2 Delete Cancel Sort User View Size 11 LastUsed 03 04 00 exp000 exp001 exp002 adrian adrian adrian 10 12 13 02 22 00 02 10 00 02 02 00 Methods and Users 4 23 4 Use the arrow keys to highlight the method you want to delete then press F1 Delete The Delete Method screen appears 5 Press F1 Yes to delete the method After the method is deleted the Stored Methods screen appears Note Even after you delete the last method stored under a user name the name is not removed from the instrument To delete the name see Deleting a User Name on page 4 5 To delete a method continued Step Action Press Yes to delete the method Delete Method Methods on In
30. a time or temperature at the completion of each cycle Name and store the method See Chapter 5 08 00 AM 09 25 00 25 0 C GeneAmp PCR System 2700 User adrian F1 F3 F4 F5 F2 Run User Util Edit Create Version Configure your instrument time date pause time out etc Use the Tm calculator Delete a method View history of the last method run Perform hardware diagnostics display and keypad Run system performance tests heating and cooling rate and cycle time Run temperature verification and temperature uniformity tests Upgrade firmware See Chapter 6 See Chapter 5 Utilities Applied Biosystems Thermal Cycler 1 6 System Overview Introducing an Important Screen Create Edit Screen One of the features that makes the 2720 Thermal Cycler easy to use is its graphical representation of a method as shown below on the Create Edit screen The graph is the wavy line 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 On the Create Edit screen temperatures are shown above the graph in degrees Celsius Hold times in minutes and seconds are shown below the graph The central portion of the screen delineated by dashed lines is the PCR segment In this example the PCR segment repeats 25 times After PCR in the post PCR segment the instrument holds the samples at 72 C for 7 minutes then cools to 4
31. at 11 30 05 AM 02 01 00 Length of run is 01 34 25 End of Run F1 F3 F4 F5 F2 Hist Exit Method Not Stored Press Store to save the method Press Exit to delete the method F1 F3 F4 F5 F2 Exit Store Methods and Users 4 1 Methods and Users 4 Overview About This Chapter This chapter provides procedures for creating and editing a method whether it is simple or more complex Procedures for adding and handling user names are also included In This Chapter This chapter contains the following topics Topic See Page Adding Changing or Deleting a User Name 4 2 Creating a Method 4 6 Changing a Method Using Advanced Features 4 9 Handling Methods 4 18 4 4 2 Methods and Users Adding Changing or Deleting a User Name Introduction On the Applied Biosystems 2720 Thermal Cycler methods are stored by both method name and user name It s important to have your own user name to keep your methods separate from those belonging to other users Even if you are the only user of the system you still need a user name A user name can be added as well as changed or deleted You can protect your user name by having a PIN number When a PIN number has been created only the person who knows the PIN number can change the user name Additionally once you have PIN the system allows you to lock your methods When your methods are locked only the person who knows the PIN number can overwrite or delete t
32. hardware and software be restored to the standard configuration prior to providing service or technical support For systems that have built in computers or processing units installing unauthorized hardware or software may void the Warranty or Service Plan Limited Product Warranty Limited Warranty Applied Biosystems warrants that all standard components of the GeneAmp PCR Instrument Systems and Veriti Thermal Cyclers will be free of defects in materials and workmanship for a period of one 1 year from the date the warranty period begins unless otherwise stated Applied Biosystems will repair or replace at its discretion all defective components during this warranty period After this warranty period repairs and replacement components may be purchased from Applied Biosystems at its published rates Applied Biosystems also provides service agreements for post warranty coverage Applied Biosystems reserves the right to use new repaired or refurbished instruments or components for warranty and post warranty service agreement replacements Repair or replacement of products or components that are under warranty does not extend the original warranty period Applied Biosystems warrants that all optional accessories supplied with its GeneAmp PCR Instrument Systems and Veriti Thermal Cycler such as peripherals printers and special monitors will be free of defects in materials and workmanship for a period of ninety 90 days from the date
33. instrument AVERTISSEMENT Pour viter les chocs lectriques d brancher le cordon d alimentation avant le d pannage Fire Hazard 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 AVERTISSEMENT Afin d assurer la protection contre les risques d incendie remplacer uniquement par un fusible de m me type et de m me courant nominal GR1987 3 pronged power cord receptacle Power on off switch GR1987 Fuse compartment DRAFT October 22 2010 3 44 pm Safety_HW fm xx Laboratory Environmental Requirements Temperature Humidity and Environment IMPORTANT This instrument is designed for indoor use IMPORTANT Do not operate in a Cold Room or a refrigerated area The 2720 Thermal Cycler will operate safely when the ambient temperature is 5 C to 40 C 41 F to 104 F and will meet performance specifications when the ambient temperature is 15 C to 30 C and the ambient relative humidity is 20 to 80 These specifications have been calculated for altitudes between 0 and 2 000 meters FIRE HAZARD This instrument is not designed for operation in an explosive environment Do not place the instrument close 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 00
34. or use an empty tray and cover the wells with caps or the full plate cover Close the heated cover and pull the lever down Both of these tests are performed from the System Performance screen Running the Rate Test Use the Rate Test to verify that the Peltier units are operating correctly The test takes approximately two minutes to run System Performance Rate Cool and Heat Rate Test Cycle Cycle Performance Test F1 F3 F4 F5 F2 Rate Exit Cycle To run the Rate Test Step Action 1 Access the Warning screen a From the Main Menu press F4 Util to access the Utilities 1 screen b Press F1 Diag to display the Diagnostics screen c Press F2 System to display the System Performance screen d Press F1 Rate The Warning screen appears 2 After you have installed a plate and cover press F1 Cont The instrument then runs through a series of tests where the sample block is stabilized at 35 C 94 C and 4 C WARNING Install an empty Microplate F1 F3 F4 F5 F2 Cancel Cont with a MicroAmp Full